It comes down to copyright law. It's a remix (and from what I heard, more sampling than remix) and not the original song. I'm not a media lawyer, but I deal with it enough working at a radio station to know about the nasty world of royalties. If Sega puts an original ROM image on an emulator, there was a contract previously agreed to for sales of that game which they abide by. If they want to remake/reuse the music in another work, a new agreement has to be made with the original artist. The Sonic CD re release is a remake using a new game engine. That means the soundtrack has to be licensed to be used. Spencer Neilson/Pastiche would need to negotiate for their works to be used. That's why there was a revision to Sonic Spinball since Sega does not own the Sonic 1 title theme. Since the Japanese soundtrack was made by people employed by Sega there is no problem using those tracks. Spencer Neilson also worked for Sega at the time but anytime vocals by Pastiche are used, they would have to be compensated for their contributions (It's no different than if they had Madonna sing instead.) It's easier (cheaper) for Sega to use the JP/EU soundtrack than to try and use the US soundtracks.
This stuff goes on all the time behind the scenes with games, but never is looked at as much as the differences between the beta and final game.