Why do you think projects like Sonic 4 and Mania have Sky Chase references? My understanding is it's not well-remembered but then I personally think it's the worst stage in the Genesis games so I'm biased.
I don't think it's a great level either, but it's variety. It's something different. A palette cleanser. Something to clear your head with. That makes it memorable, I think, but I think modern interpretations misunderstand its role as a palette cleanser. Especially the Sonic 4 games, where they try to "improve" its gameplay.
I think it's meant to be a moment to encourage reflection, to make you realize how far you've come, and make you wonder what other tricks the game still has up its sleeve if it's changing things this much 16 or 17 levels into the game. You are far from where you've started, far from home, and there's no turning back now.
Those games simply reference it because it's a notable thing from one of the best games.