Wait wut Sonic 3 in Gems? O_o
Anyways I don't really know the answer, but it might be different in S3K. There is one main difference in S3K LB2 (opposed to S3 LB2) that I know, but that's at the end. (In S3K, the clock stops after the first boss and starts again at the beginning of the second.)
Don't know about this top of screen glitch though.
The map doesn't really give away anything from what I can see though. (And why would it.) Unless it has a glitch similar to that of the Sky Sanctuary screenwrap glitch, where you can't see yourself but you can hit an obstacle (or wall), and I can see one place where that's possible. That doesn't really explain a difference between two versions though. >_>