Well Mr. zerow, I've tried out this M4A format and it seems to behave in Mp3tag similar as APE- you have to stop the file before changing a tag value in it. Which of course will make you loose a ton of time and completely disrupt my workflow; I mean your workflow
But I've also tried out the WMA format in 9.2 lossless version. And it seems to works exatly [in terms of playing and metadata retaining] the same way as MP3 and FLAC. And also making an "encoding test loop" FLAC > WAV > WMA > WAV resulted in showing two same audio waveforms in those two WAV files after loading them into a sound editor
So all you need now is some hardcore Mp3tag users to confirm that usability of WMA's; the no tag-issues statement of some sort from them would probably put your mind at ease