Saying different engines is hard to say, because technically it is the same engine, but the gameplay for the bosses is different.  Basically the boss engine will play similar to what you see in the magazine screen shots of Metal Sonic and Nack.

I don't want to say too much because, thanks to a few email back and forwards we have inside information on how the boss battles worked, and I kind of want to keep it a surprise till the games release.