Okay, this needs to be bumped. Let's just make this a general "who composed Sonic 3?" topic.
https://www.youtube.com/playlist?lis...el8PBU2hxgdd7n
A proto of Sonic 3 has surfaced. Turns out the "new" music for Sonic & Knuckles Collection was actually the original stuff (though the PC versions of the songs are arranged somewhat). This also includes the "new" midboss theme that appears in Sonic & Knuckles; that's in here too. This seems to confirm that there was some kind of issue with having "the MJ music" (I'm aware of Hard Times) at some point after Sonic 3, and that "the MJ music" was brought in later.