As far as I can understand, there is not a way to "passthru" FLAC audio, but only re-encode it? It seems the downsides to that is that the channel positions are not retained (at least as far as I can tell using MediaInfo) and the minor inconvenience of having to first determine the bit rate of the source FLAC before selecting either 16 or 24-bit in Handbrake. And the extra time needed to re-encode but that's not as much an issue for me.
What I'm doing now is creating the file with MakeMKV (with FLAC audio) and would love to be able to just run that through Handbrake to re-encode the video and basically not touch the audio.
FLAC passthru Q
Re: FLAC passthru Q
Use MKVtoolnix and MKVmergegui to multiplex in the original audio after the encode (assuming you're targeting MKV), and remove the audio track in Handbrake encode, since there's no FLAC passthrough.