Why is the S&K miniboss music in Sonic 3? (Hydrocity miniboss)

*Edited the above post with more information and analysis straight from the ASM.

 

My complete speculation without evidence would be that the Sonic & Knuckles was the prototype music that they were in the middle of replacing with the new tracks, the ones in Sonic the Hedgehog 3's release, hence it being the music playing in the recent November 3rd, 1993 prototype. Things happened and they couldn't get the prototype track out nor replace all the music IDs before they had to ship it as is.

When they decided to change direction with the music team for Sonic & Knuckles, they simply did a Sonic Origins and replaced the music with the prototype, since they didn't need to reimplement it: it was still in there.