Though I'd spent a good deal of time wrestling with the poorly documented Apple Lossless format, I decided to take a break and finally get Ogg FLAC working. Although the 'flac' binary does a great job of encoding and decoding them, there simply isn't an existing tool to edit Ogg FLAC metadata. So, I adapted my routines to set Ogg Speex metadata to Ogg FLAC and now everything is working properly except for ReplayGain (which I'll need to calculate by hand).
I've also shifted all of the audio formats into individual sub-modules instead of letting audiotools/__init__.py grow even more huge. Though I've run all sorts of quick & dirty tests, I expect there's still some breakage I've yet to find.
Once I make sure everything's working correctly, I'll call it 2.3 and release it to the world.