I am curious if the early build of the sound driver supports the MJ/Buxer soundtrack and perhaps that's yet another reason why the earlier tracks are still in the game.
Yea, they can, you'd just also have to make sure you get all the necessary data ported over, such as samples. It's just the final's sound driver but with more bugs. I dunno why an early version of a sound driver would be a reason why those tracks were still in the game, though, unless they were planning to completely overhaul the driver and didn't want to waste time implementing the new tracks in thate old one. Judging from how late the proto was and how development was going at the time, completely overhauling the sound driver would've been a monumentally stupid idea.
The S3 Final music will work in S3B, but you will have to remap the DAC samples from the final tracks to ones that exist in S3B. S3B has the final DAC samples but only up to ID 9B, so Ice Cap, Carnival Night, Launch Base, Knuckles' theme, and the Credits theme from the final version will be broken.