How to make Apple Mail.app to use SOCKS proxy configured by a PAC file
Try go to Network Preferences, select the network you want to set, and go to Advanced -> Proxies. Then, set both Automatic Proxy Configuration and SOCKS proxy. It works for me.

FYI, if you're using Shadowsocks the PAC would probably be http://127.0.0.1:8090/proxy.pac.