On the optional components page of foobar's web site it says it has stability issues, but aside from that, would M4A files that I wish to play in foobar sound the same then if I were to install iTunes and play the files from there? The reason I ask is because I a few ALAC songs from when I used iTunes on a previous format on my computer, and I wish to convert them to FLAC. Would all quality be retained?

I was also interested in this, so I took a a 44100Hz, 16bit wav file, used iTunes to convert to ALAC, then loaded the ALAC and the original WAV into foobar 0.9 and used the 'bit compare tracks' function. No differences were found. However this might not always be the case, but I used an entire CD image for the test, so I'd say it's likely that it is accurate.