There are two ways to do this, the first is the one you mention, but seem hesitant to use. It can be done at the AMA stage or after the transcode.
1. Select all clips,unlink, modify to tracks to VA1A2, then relink. This only changes the master clip relationship to the media, and does not delete the media.
2. Subclip VA1A2 from each clip. This could be done on a per clip basis which is quite tedious, or could be done as an ALE export/Import Merge process. Since v7.0.3. ALE merge is non-destructive to existing metadata already logged which makes this a very good alternative if you are comfortable with text editing. Open bin with master clips. Make sure Bin columns include Tape, Source File, Start, End, Tracks, Name. Select clips and export as ALE. In a text editor, replace the value found in tracks with VA1A2 (search and replace function). With clips still selected, go to import settings Shot Log” and select the one that says something along the lines of “merge with known sources and create subclips”. I am not in front of my system right now, but it will something like that. Bin will now have your original master clips, and then 1 new subclip for every master clip that is only VA1A2. Edit from those.
Michael