FLAC will do the same, but then your ATV will turn its nose up at your tracks and won't play them. One solution might be to get a media server package on the NAS able to transcode on the fly, so you point your non-Apple devices at that one, and they see a format they can handle.
I believe the Synology can be set up to transcode to PCM on the fly, which would be a solution, but I'm not entirely sure about the set-up for this. Will do some reading and come back to you – unless a Synology owner would like to chime in?
Will the MinimServer you mentioned elsewhere not do the trick? Seems great.
Arcam Solo Mini/Monitor Audio RX1/Cambridge Audio 751BD/Samsung 37” LCD
Well I've had a play with converting a few tracks to FLAC and my Apple TV / XBMC plays them fine. So that's an option, but then each time I rip a CD to iTunes I'll have to convert it before sending to my NAS which would be a pain.
However, I've installed the Audio Centre on the NAS and have downloaded the Synology Android app and this quite happily plays the Apple Lossless files so perhaps the problem is solved that way...
Synology DS212J-> AppleTV-> rDAC->Naim Nait5i. Naim CD5i. Dynaudio Audience 52SE
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Alternatively rip in dual format and manually add the new rips to iTunes.
Mac mini > AVI ADM9Ts
From the moment I started my digital collection I knew I'd have format issues later on down the line - which was why I ripped FLAC, ALAC and 320k MP3 versions of all my music. Sure, it takes up a little more space but it's saved me so many headaches, what with Android, Apple and Microsoft all under my roof!
The majority of my music is stored on my Synology NAS in FLAC format. The iTunes Server allows iTunes (and thus the ATV when iTunes is open on the MBP) to see the library as a shared library on the NAS. I am not sure but I think it converts the FLAC files to WAV 'on the fly'.
Alternative is to 'push' the FLAC files to the ATV using Synology DS Audio app on IOS device.
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If I were you I would rip in ALAC and MP3 (320 Kbps).
Play the MP3 where the ALAC doesn't work. They sound the same anyway imo, but you also have a lossless version for archive or transcoding later.
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