Reading the Australian manual (thank you Batpig), it's nice to see the support for Apple Lossless (up to 96 kHz) from the USB/NAS etc. One can always use a Apple TV or Airport Express to get around this, but those are limited to 48 kHz. It doesn't state 24-bit so I hope it is not limited to 16-bit. And the optical out from a AE cannot be distributed to zone 2/3, while the network input can.
Strangely enough it doesn't support the uncompressed Apple format: AIFF. I use both ALAC and AIFF. Fair enough, I can always convert. Never noticed difference in SQ. Just figured AIFF would be more universal. Yeah right. Other devices support AIFF, but not ALAC (Cambridge Audio, I believe)!
I think that the standard lossless format these days is FLAC. Like everything with crApple, AIFF, ALAC, etc is just too proprietary. As long as it supports FLAC, that's really all that matters. And that crApple devices don't support FLAC is the reason why I avoid any of their products (and iTunes is simply THE worst piece of software in existence!).