Ahhh, I just discovered something I wasn't aware of -- The enhanced commentary isn't "just" commentary!

I was under the impression it was merely an audio track that lined up with the original movie timing, much like most movie's commentary tracks. However, it's actually an "interactive" movie, so to speak, with the commentators pausing the movie and drawing/diagramming things on the screen. So it wouldn't really be feasible to strip merely the audio track and fuse it into the original bluray rip.

Unless anyone has any ideas, I guess this means we just have to keep the two separate movies? I've wondered if perhaps there's some trickery possible of "fusing" the two tracks of video, so that you can have the option of watching the commentary-edition and have it actively inject the commentary clips of movie-pausing and diagramming. But I imagine something like this wouldn't be possible, or at least feasible.