Firstly, I have to say I'm a big fan of the original version of the patch since it fixes a major issue with FF6A, so I look forward to these fixes. The sync issues were basically the only problems I had with 1.0.
Regarding the specific issues you bring up there, I don't think I ever noticed there were more people singing in the Japanese version than those who appeared on screen during the opera (if you mean it happens even in v1.0 and not just due to the fixes you'd be making). Obviously, I did notice the sync issue though. If it is present in 1.0 and they're just background singers rather than anyone having a solo role, then I may have noticed it but just didn't have a problem with it, since background singers could often be offstage or something. If it was someone with a solo role, then with just a casual listen I probably couldn't tell their voices apart from those of the primary characters who were on screen =P (Ralse, Celes, Draco, etc.) Since most of us don't understand Japanese, male voices will sometimes sorta be able to blend in with other male voices which don't sound too different and females with other females as long as the text is appearing while the lines are sung and disappears during periods of silence.
Anyway, I don't really like the idea of a mix of both versions if lyrics sung in both Japanese and English will be in there. That'd probably seem somewhat unprofessional and unnatural, although I can't entirely judge until I've seen it. (However, if an instrumental portion from, say, the English version would fit in un-awkwardly somewhere to replace a part of the Japanese instrumental segments and make the sync issue easier to fix then I'd say that'd likely be fine.)
Since the lyrics are different with the intro portion of the English opera, that might be a problem professionalism-wise too if you used the english audio. I wonder, however, if you might consider changing the text lines of that portion in FF6A to the ones sung in the audio file. I understand if that's a no-go though, since it might be altering a part of the game you don't really feel is part of the scope of this patch. Or it might be a no-go depending on what lines are being changed, since people familiar with that translation would notice it. Even barring that, it could be a no-go due to space issues in the opera segment of the script as well.
If not, then I'd say it'd probably be best just to go with the Japanese version with fixed sync.
When I saw the sync issue, however, I had wondered why it wasn't possible instead just to duplicate the SNES sound chip opera (garbled voices and all) in the same way the other songs were duplicated, but that sorta gets into the mechanics of making a patch like this one which I recognize I don't fully understand. I didn't realize you'd need to get sampling from real instruments to do so. To be perfectly honest, I'd probably prefer a version that does that over a streaming audio version with the real orchestra, since my priorities are mostly just making the game more like the SNES version. I understand if that isn't possible however. Although using the streaming audio version of the opera on the SNES FF6 OST would probably achieve basically the same thing. I guess you didn't feel that was the right way to go since you don't care too much for the garbled SNES voices or felt most people don't?
Regarding the FF5A patch, I haven't played FF5A with the old patch, so if I were to replay FF5 some time in the future, I'd probably use the newer one. I suppose you could chalk that up as at least one person who would use an improved version of the patch, but I have no idea whether I'm in the majority or minority there.