No multi-channel FLAC for music files on Plex Android TV clients (Nvidia Shield, Amazon Fire devices, Sony TVs, etc). I found a post from May where I tested it. I’m not aware of any changes. A quick forum search did not turn up anything, and nothing is mentioned in the announcement thread.
Plex HTPC on Windows 10 seems to support multi-channel FLAC music files. See this post from August.
There is also the Plexamp audio player. I’ve never used it, so not sure how it handles multi-channel FLAC. The Android app is only for mobile devices (Google won’t download it to my Shield). Other platforms might be an option.