How to add AAAA flag (IPv6) to DNS resolver configuration on Sierra?
This was a huge hassle to figure out, so I wrote up a little guide in hopes that others would find it helpful:

How to convince macOS to do IPv6 DNS lookups when your only IPv6 address is via a VPN or tunnel of some sort

The Problem

macOS's domain name resolver will only return IPv6 addresses (from AAAA records) when it thinks that you have a valid routable IPv6 address. For physical interfaces like Ethernet or Wi-Fi it's enough to set or be assigned an IPv6 address, but for tunnels (such as those using utun interfaces) there are some extra annoying steps that need to be taken to convince the system that yes, you indeed have an IPv6 address, and yes, you'd like to get IPv6 addresses back for DNS lookups.

I use wg-quick to establish a WireGuard tunnel between my laptop and a Linode virtual server. WireGuard uses a utun user-space tunnel device to make the connection. Here's how that device gets configured:

utun1: flags=8051&lt;UP,POINTOPOINT,RUNNING,MULTICAST&gt; mtu 1420
    inet 10.75.131.2 --&gt; 10.75.131.2 netmask 0xffffff00
    inet6 fe80::a65e:60ff:fee1:b1bf%utun1 prefixlen 64 scopeid 0xc
    inet6 2600:3c03::de:d002 prefixlen 116
    nd6 options=201&lt;PERFORMNUD,DAD&gt;


And here's a few relevant lines from my routing table:

Internet:
Destination        Gateway            Flags        Refs      Use   Netif Expire
0/1                utun1              USc             0        0   utun1
default            10.20.4.4          UGSc            0        0     en3
10.20.4/24         link#14            UCS             3        0     en3      !
10.75.131.2        10.75.131.2        UH              0        0   utun1
50.116.51.30       10.20.4.4          UGHS            7  2629464     en3
128.0/1            utun1              USc             5        0   utun1

Internet6:
Destination                             Gateway                         Flags         Netif Expire
::/1                                    utun1                           USc           utun1
2600:3c03::de:d000/116                  fe80::a65e:60ff:fee1:b1bf%utun1 Uc            utun1
8000::/1                                utun1                           USc           utun1



10.20.4/24 is my local ethernet network.
10.20.4.5 is my laptop's LAN IP address.
10.20.4.4 is my gateway's LAN IP address.
10.75.131.2 is the IPv4 address of my end of the WireGuard point-to-point tunnel.
2600:3c03::de:d002 is the IPv6 address of my end of the WireGuard point-to-point tunnel.
50.116.51.30 is the public address of my Linode server.


This should be enough to have IPv6 connectivity, right? Well, name resolution works when host talks directly to my name server:

sam@shiny ~&gt; host ipv6.whatismyv6.com
ipv6.whatismyv6.com has IPv6 address 2607:f0d0:3802:84::128


Pinging by IPv6 address works:

sam@shiny ~&gt; ping6 -c1 2607:f0d0:3802:84::128
PING6(56=40+8+8 bytes) 2600:3c03::de:d002 --&gt; 2607:f0d0:3802:84::128
16 bytes from 2607:f0d0:3802:84::128, icmp_seq=0 hlim=55 time=80.991 ms

--- 2607:f0d0:3802:84::128 ping6 statistics ---
1 packets transmitted, 1 packets received, 0.0% packet loss
round-trip min/avg/max/std-dev = 80.991/80.991/80.991/0.000 ms


And HTTP connections by IPv6 address work:

sam@shiny ~&gt; curl -s 'http://[2607:f0d0:3802:84::128]' -H 'Host: ipv6.whatismyv6.com' | html2text | head -3
                 This page shows your IPv6 and/or IPv4 address
                          You are connecting with an IPv6 Address of:
                                             2600:3c03::de:d002


However, HTTP connections by IPv6-only hostname don't work:

sam@shiny ~&gt; curl 'http://ipv6.whatismyv6.com'
curl: (6) Could not resolve host: ipv6.whatismyv6.com


The result is the same in wget as well as in GUI apps like Firefox: connecting by a literal IPv6 address works fine, but connecting by a hostname that only has an AAAA record (and no A record) associated with it does not.

Interestingly, ping6 is able to do a DNS lookup and get an IPv6 address back:

sam@shiny ~ [6]&gt; ping6 -c1 ipv6.whatismyv6.com
PING6(56=40+8+8 bytes) 2600:3c03::de:d002 --&gt; 2607:f0d0:3802:84::128
16 bytes from 2607:f0d0:3802:84::128, icmp_seq=0 hlim=55 time=49.513 ms

--- ipv6.whatismyv6.com ping6 statistics ---
1 packets transmitted, 1 packets received, 0.0% packet loss
round-trip min/avg/max/std-dev = 49.513/49.513/49.513/0.000 ms


Why can ping6 do this when nothing else can? It turns out that when ping6 calls getaddrinfo it overwrites the default flags. One of the default flags is AI_ADDRCONFIG, which tells the resolver to only return addresses in address families that the system has an IP address for. (That is, don't return IPv6 addresses unless the system has a (not link-local) IPv6 address.) Most other programs add to the default flags rather than clobbering them, which I suppose is sensible.

If you run scutil --dns it will tell you how the resolver is set up. Here's the output on my system (minus a bunch of mdns stuff that doesn't matter):

DNS configuration

resolver #1
  search domain[0] : home.munkynet.org
  nameserver[0] : 10.20.4.4
  if_index : 14 (en3)
  flags    : Request A records
  reach    : 0x00020002 (Reachable,Directly Reachable Address)

DNS configuration (for scoped queries)

resolver #1
  search domain[0] : home.munkynet.org
  nameserver[0] : 10.20.4.4
  if_index : 14 (en3)
  flags    : Scoped, Request A records
  reach    : 0x00020002 (Reachable,Directly Reachable Address)


Note that under flags, it says Request A records but not Request AAAA records. So it's left to us to try to convince macOS's resolver that we do in fact have a valid IPv6 address, even though it's on a tunnel interface.

SystemConfiguration

The "right" way for this to happen is for whatever program sets up the tunnel to use the bizarre and largely undocumented SystemConfiguration API to register the network "service" and its IPv6 properties. The Viscosity app does this. Tunnelblick does not, the official OpenVPN Client does not, and wg-quick sure as hell doesn't.

The scutil Kludge

We can create the same SystemConfiguration "service" strucures manually using the scutil command:

First we create the IPv4 part of the service:

sam@shiny ~&gt; sudo scutil
&gt; d.init
&gt; d.add Addresses * 10.75.131.2
&gt; d.add DestAddresses * 10.75.131.2
&gt; d.add InterfaceName utun1
&gt; set State:/Network/Service/my_ipv6_tunnel_service/IPv4
&gt; set Setup:/Network/Service/my_ipv6_tunnel_service/IPv4


And then we create the IPv6 part:

&gt; d.init
&gt; d.add Addresses * fe80::a65e:60ff:fee1:b1bf 2600:3c03::de:d002
&gt; d.add DestAddresses * ::ffff:ffff:ffff:ffff:0:0 ::
&gt; d.add Flags * 0 0
&gt; d.add InterfaceName utun1
&gt; d.add PrefixLength * 64 116
&gt; set State:/Network/Service/my_ipv6_tunnel_service/IPv6
&gt; set Setup:/Network/Service/my_ipv6_tunnel_service/IPv6
&gt; quit


Once this is done, the output of scutil --dns (again modulo mdns stuff) changes:

DNS configuration

resolver #1
  search domain[0] : home.munkynet.org
  nameserver[0] : 10.20.4.4
  if_index : 14 (en3)
  flags    : Request A records, Request AAAA records
  reach    : 0x00020002 (Reachable,Directly Reachable Address)

DNS configuration (for scoped queries)

resolver #1
  search domain[0] : home.munkynet.org
  nameserver[0] : 10.20.4.4
  if_index : 14 (en3)
  flags    : Scoped, Request A records
  reach    : 0x00020002 (Reachable,Directly Reachable Address)


Now we see Request AAAA records in the flags! I'm not really sure what "scoped queries" are or why the DNS configuration for them didn't change, but things seem to work now so whatever:

sam@shiny ~&gt; curl -s 'http://ipv6.whatismyv6.com' | html2text | head -3
                 This page shows your IPv6 and/or IPv4 address
                          You are connecting with an IPv6 Address of:
                                             2600:3c03::de:d002


When disconnecting from the tunnel, all you have to do is remove the SystemConfiguration keys you added:

sam@shiny ~&gt; sudo scutil
&gt; remove State:/Network/Service/my_ipv6_tunnel_service/IPv4
&gt; remove Setup:/Network/Service/my_ipv6_tunnel_service/IPv4
&gt; remove State:/Network/Service/my_ipv6_tunnel_service/IPv6
&gt; remove Setup:/Network/Service/my_ipv6_tunnel_service/IPv6
&gt; quit


A couple things to note:


The name my_ipv6_tunnel_service is totally arbitrary.
According to information I gleaned from the up/down scripts in the Mullvad .ovpn profile, you have to create both the Setup: and State: keys. I didn't verify this because I am lazy.
I have no clue where the IPv6 DestAddresses come from. I copied these from Viscosity because they seemed to work there. ::ffff:ffff:ffff:ffff:0:0 for the link-local address and :: for the public 
I don't even really know what DestAddresses means or what it's used for.


A nice script

I wrote a python script that gleans addresses and prefix lengths from ifconfig output. It requires Python 3.6 or later so make sure you've got that in your path. It's called wg-updown and calls its SystemConfiguration service wg-updown-utun#, but it's not really WireGuard-specific. You could call it as a post-up/pre-down script for any old VPN tunnel or run it manually. Call it like this:

# After tunnel comes up
wg-updown up IFACE

# Before tunnel goes down
wg-updown down IFACE


replace IFACE with the name of the interface that your tunnel/VPN client is using, e.g. utun1. It will print the commands that it's sending to scutil so you can see what it's doing in detail.

#!/usr/bin/env python3

import re
import subprocess
import sys

def service_name_for_interface(interface):
    return 'wg-updown-' + interface

v4pat = re.compile(r'^\s*inet\s+(\S+)\s+--&gt;\s+(\S+)\s+netmask\s+\S+')
v6pat = re.compile(r'^\s*inet6\s+(\S+?)(?:%\S+)?\s+prefixlen\s+(\S+)')
def get_tunnel_info(interface):
    ipv4s = dict(Addresses=[], DestAddresses=[])
    ipv6s = dict(Addresses=[], DestAddresses=[], Flags=[], PrefixLength=[])
    ifconfig = subprocess.run(["ifconfig", interface], capture_output=True,
                              check=True, text=True)
    for line in ifconfig.stdout.splitlines():
        v6match = v6pat.match(line)
        if v6match:
            ipv6s['Addresses'].append(v6match[1])
            # This is cribbed from Viscosity and probably wrong.
            if v6match[1].startswith('fe80'):
                ipv6s['DestAddresses'].append('::ffff:ffff:ffff:ffff:0:0')
            else:
                ipv6s['DestAddresses'].append('::')
            ipv6s['Flags'].append('0')
            ipv6s['PrefixLength'].append(v6match[2])
            continue
        v4match = v4pat.match(line)
        if v4match:
            ipv4s['Addresses'].append(v4match[1])
            ipv4s['DestAddresses'].append(v4match[2])
            continue
    return (ipv4s, ipv6s)

def run_scutil(commands):
    print(commands)
    subprocess.run(['scutil'], input=commands, check=True, text=True)

def up(interface):
    service_name = service_name_for_interface(interface)
    (ipv4s, ipv6s) = get_tunnel_info(interface)
    run_scutil('\n'.join([
        f"d.init",
        f"d.add Addresses * {' '.join(ipv4s['Addresses'])}",
        f"d.add DestAddresses * {' '.join(ipv4s['DestAddresses'])}",
        f"d.add InterfaceName {interface}",
        f"set State:/Network/Service/{service_name}/IPv4",
        f"set Setup:/Network/Service/{service_name}/IPv4",
        f"d.init",
        f"d.add Addresses * {' '.join(ipv6s['Addresses'])}",
        f"d.add DestAddresses * {' '.join(ipv6s['DestAddresses'])}",
        f"d.add Flags * {' '.join(ipv6s['Flags'])}",
        f"d.add InterfaceName {interface}",
        f"d.add PrefixLength * {' '.join(ipv6s['PrefixLength'])}",
        f"set State:/Network/Service/{service_name}/IPv6",
        f"set Setup:/Network/Service/{service_name}/IPv6",
    ]))

def down(interface):
    service_name = service_name_for_interface(interface)
    run_scutil('\n'.join([
        f"remove State:/Network/Service/{service_name}/IPv4",
        f"remove Setup:/Network/Service/{service_name}/IPv4",
        f"remove State:/Network/Service/{service_name}/IPv6",
        f"remove Setup:/Network/Service/{service_name}/IPv6",
    ]))

def main():
    operation = sys.argv[1]
    interface = sys.argv[2]
    if operation == 'up':
        up(interface)
    elif operation == 'down':
        down(interface)
    else:
        raise NotImplementedError()

if __name__ == "__main__":
    main()