for your #5 above...
no, i doubt it. My guess is that it tags the files with it's own id3v2 frame. hopefully, that tag is id3v2.3, which winamp3 recognizes, and not id3v2.4, which it will not (is that correct Sawg?). You can make a copy of a file, convert it to atrac, and see if it loads the id3 in wa3. if not, delete it, and never do it again.
I also suggest that you don't need to keep those atrac files, since they will be of lower quality than the mp3's they came from (as with converting between any two lossy formats).