If you are OK with 16/48, the newest AppleTV will play back lossless 5.1. You just have to convert it from flac to Apple Lossless and get the channel order right. It won't playback 4 channel correctly, but 5.0 and 5.1 work fine. Apple wants the channel order to be C, L, R, LR, RR, LFE. I've tested up to 24/192 but as I said the AppleTV will down convert it to 16/48.
The only tool I know that will convert from multichannel flac to multichannel Apple Lossless and map the channel order correctly is xACT. You then have to change the extension from .m4a to .m4p for iTunes and the AppleTV to recognize them.
The only tool I know that will convert from multichannel flac to multichannel Apple Lossless and map the channel order correctly is xACT. You then have to change the extension from .m4a to .m4p for iTunes and the AppleTV to recognize them.