Well, specifically I think the crosstalk and delay tends to make music come out with less clarity. I think sound effects benefit from the rear spatial effect in a way that music mostly doesn't.
However, I'm sure many people prefer how some music sounds through pro-logic decoding. Often even if it wasn't intended for that form... it was kinda advertised as a thing that would "add" surround to your existing stuff. I think most people who had a home theatre with this option would just turn it on and leave it on, they wouldn't check which VHS tapes had the dolby logo and only use it for those.
My personal feeling is that if the music was composed for stereo and pro-logic decoding is imposed on it after the fact, you're losing something in the crosstalk. But... I dunno, it's not terrible. It's basically a little bit of "echo". It's like if you brought your radio into the shower, and you liked the way it sounded in there. Maybe it does sound good, but it's definitely not the sound it was written for. If you give me the choice, I'd rather listen to the music in its original stereo form.
I don't wanna say that there's only one way to play a game. Obviously these things were made to be played on a variety of home setups. Not something I can prove, but I suspect most of the SNES games with dolby surround support were primarily made with stereo in mind. People did/do have surround sound in their homes, but it's always been a minority. My feeling is that this stuff was made in stereo, and still sounded OK with pro-logic going on. The effect is certainly subtle enough to not normally be a big problem either way.
Looking at Vortex and its music. It looks like when you set it to stereo mode, they universally have the right echo channel inverted, sending all echoes to the rear. That seems to be the entirety of the effect on the music. All of the music has lots of echo with stereo panning. Clearly they tried to make something that would enhance the spatial effect of pro-logic surround. On a regular stereo system the echo would probably have some spatially-sensitive destructive interference, but given what they were going for was mostly just a full and bubbly stereo field of echoes, that shouldn't be too bad of an effect?
I also looked at Seiken Denestsu 3, and interestingly it has options for mono, stereo, and wide-stereo. The wide version appears to just globally invert the left channel and nothing else! Quite a strange effect... You definitely wouldn't want this by default, because it could cause centre channels to drop entirely on mono systems. To set the "wide" version on most stereo speaker setups is probably less than ideal (destructive interference), but on headphones it gives a different "inside the head" spatial effect. Does SD3-wide actually sound any good on dolby? I feel like what it's doing would send far too much of the sound to the rear? (I almost wish I still had my old surround system that had pro-logic to test with now, but I got rid of it years ago.)
Secret of Mana was also on some lists, but I don't see why? It doesn't have any audio settings in the game, and I didn't catch it using inverted audio at all. It doesn't have a dolby logo on the box, either.