lightning daemon rejects bitcoind RPC variables in lnd.conf
Found out that any bitcoind.XXX options need to be under a [Bitcoind] heading. Working lnd.conf is as follows:

[Application Options]
debuglevel=info
debughtlc=false
maxpendingchannels=5
alias=WittyAlias
color=#000300
maxlogfiles=3

[Bitcoin]
bitcoin.active=1
bitcoin.node=bitcoind
bitcoin.mainnet=1

[autopilot]
autopilot.active=1
autopilot.maxchannels=16
autopilot.allocation=0.1

[Bitcoind]
bitcoind.rpchost=127.0.0.1:8332
bitcoind.rpcuser=wittyusername
bitcoind.rpcpass=VerySecretSuperDuperRPCauthPassword
bitcoind.zmqpubrawblock=127.0.0.1:28332
bitcoind.zmqpubrawtx=127.0.0.1:28333