Amazing comparisons, laffer!
I grew up with Sound Blaster for my old DOS games, and I have never known about the MT-32 until a few years ago; haven't even heard one in action until just now! I must admit, it is one hell of a massive improvement over that garbly FM Synthesis that the Adlib was putting out. It's kind of funny how I used to own a Genesis/Megadrive and a Super Nintendo, and some of the games on those systems had better audio quality than nearly all of my DOS games with Adlib/Sound Blaster.
That said, however, even the MT-32 has its drawbacks, and I wouldn't be surprised if a few games had tunes that sounded even worse than its Adlib counterpart.
EDIT: I do have a few suggestions. Can you try recording the Wing Commander games on MT-32? Would love to see how that sounds like.