The Sega CD version has far superior music. It's the same music, but it's programmed much better. This is important.
PCE-CD
Sega CD
and that's not even the most drastic one.
Also, bear in mind that the US version is the only one released for Sega CD. Curiously, there is no JP Mega CD release.
I agree that (most) of the MCD chiptunes sound better. However, that only applies to the identical songs. Thing is, you're wrong saying it's the same music. While the PC Engine version used chiptune and Redbook Audio renditions of all the music from the original PC-8801/MSX2 versions, the MCD version replaced about half the soundtrack, even some of the CD Audio tracks, and well, the actual compositions of the new tracks are not up to those of the PC88/MSX2/PCE versions.
In that sense, I'd actually say the original PC-8801 version has the best soundtrack, it has all the original tunes you'll also hear in the PCE version and they definitly sound better than the PCE chiptunes. Only the few CD Audio tracks are where the PCE version has the advantage.
PC-8801
Same track in the PCE version
You won't hear that song in the MCD version.
Oh and in the same PCE video a little bit later...
Compare this song, to...
...the one played in the same scene in the MCD version.
Not cool!