In regards to the graphical differences, they are absolutely present. Load up the PC and Dreamcast versions and go through the intro and first stage. The textures and coloring are definitely different. You should notice it right away in the scene with Chaos and the police.
What about the first level? They look similar, but there are subtle differences that were surprising to me. Take a look at the water in the PC version, for instance. It has a very different color. Same for the environment around you, which seems to be shaded in a different way.
I'm not saying either version is really any good (they both have major issues as the game itself is just broken and buggy), but they definitely changed the way the PC version looks. It's not even a port of the Gamecube version (which used a sort of "shader" effect on the water).
It's just fascinating to me that all three versions look so different. I thought the PC version was definitely the blandest of the three. It still has its own advantage in the form of a perfect framerate and better image quality, however.
I'm trying to find comparisons, but the internet wasn't the same 10 years ago and finding good SA shots on Dreamcast is proving difficult. I don't understand why people haven't posted nice VGA captured shots. Everything is a blurry composite shot, basically.