Well, first of all... where's the link for your custom sofware decoder with instructions?
The whole point of whatever passthrough engine is to avoid touching the audio, so the lack of conversion and DSP functionality would be par for the course, don't you think.
I also note that having SPDIF wav in FLAC allows one to passthrough DD, DTS and DTS 96/24 to an AVR, with no DD or DTS decoder installed in foobar.
It's probably "just" a matter to understand whether truehd atmos files are signed, unsigned, little or big endian, etc. before one can compress them with FLAC. And maybe not, I'm not sure, obviously.