Motoaki Takenouchi was a magician and a scholar. How he did the things he did with the YM2612 is anyones guess. But you are definitely right. It depends on the composer. Some Mega Drive games have shocking sound design, (the same is true of the SNES). But others make it sound like a completely different machine.
It's true that the SNES version sounds a lot meatier
Yuzo Koshiro, Motoaki Takenouchi, or practically anything by Konami in that era. Was all gold.
There is one comparison (from Konami, who by any standards at the time is a good and consistent source to judge by), and that is The Turtles in Time soundtrack vs the Hyperstone Heist Soundtrack.
Sewer Surfin (Mega Drive):
http://www.youtube.com/watch?v=ugE5l01KG5s
Sewer Surfin (SNES):
http://www.youtube.com/watch?v=fH-lLbHbG-A
Now compare both of those to the original source: Sewer Surfin (Arcade):
http://www.youtube.com/watch?v=wkWpqi0cVec
It's actually really interesting to see how this soundtrack was ported to each console.
It's true that the SNES version sounds a lot meatier and has more punch to it and audibly just sounds a lot fuller in general. But some could argue that the Mega Drive version is way more accurate in comparison to the arcade original.