The Lava Reef to Hidden Palace transition differs; in the final, the lava freezes over allowing you to walk, while, here the platform drifts over to the end of the stage, just like April 8 but with a proper functioning transition. Hidden Palace plays the Sky Sanctuary theme and has an S monitor, while Knuckles can actually punch the player out of their transformation. Sky Sanctuary is mostly like the final, with minor object differences and the Death Egg end-stage cutscene not being implemented yet.
This also shows a stark difference in Hyper Sonic's visual effects; in the final, they circle around him from top-to-bottom, while here, they use a (rather nice) pseudo 3D effect, although his afterimages are missing.