First of all, the MegaDrive game was by SEGA of America, not Konami.
Secondly, Konami were almost systematically allocating smaller ROM sizes to the MegaDrive. Hyperstone Heist plays, looks and sounds better than the SNES game, stages are longer with several scenes. However there are fewer bosses.
Tiny Toons, despite the ridiculous rom size, looks absolutely stunning. Rocket Knight Adventures shits on the Sparkster games visually speaking. And Castlevania looks perfectly fine, as well as playing much better than the two SNES games. Contra Hard Corps is another huge winner, plays like a dream. These games have MegaDrive written all over them. They run butter smooth, use the larger resolution etc...
Vastly inferior audio chip ? Seriously. They are two totally different things.
Also, don't forget that there was a strong history of Nintendo locking third parties to their consoles, and Konami only arrived on MegaDrive in 1993.