Nothing wrong with MSU-1, the nice thing about MSU-1 is you can manually replace the tracks that doesn't require much knowledge except trying to loop another song (from a player standpoint).
and I never found it immersion breaking as I get the opposite effect (especially if the music is really good and fitting) and if I found there was a song that was ill-suited for the game I would manually change it (This is why it is always a good practice to provide videos of what kind of music is inside that MSU-1 PACK in case if they have to change something manually before playing begins).
The other nice thing about MSU-1 is if you wanted to use other official tracks like importing the improved Chrono Trigger DS tracks into the SNES version you can do that, and can switch back between the two whenever you feel like it.
The choices in song quality and the instruments played does matter a lot though if you're not going to use official tracks, and that can be very tricky sometimes. My opinion when doing a MSU-1 mod is always put in various official music packs first and foremost, and then provide a experimental optional Remix Version just as a fun side-project.
Like all things MSU-1 has its Benefits and Minuses, but I find MSU-1 benefits more than it takes away, and you can adjust it when a change is needed.
On another note I didn't even know the SNES version didn't have those bonus tracks that appeared in the PSX/DS.