Ok, so you imagine it's intentionnal, but actually I was expeting a more romhacking-based technical proof that it's intentional and not just a bug.
The Playstation has only 512kb of sound RAM so the game loads different music instruments when playing a new song. Those are in the /bin/BGM/ folder. There is 81 different sound banks, but my PSF collection has 101 files, which means some of the sound banks are reused at times.
This means that when playing a music, the game loading the sound banks is probably semi-independent from loading the music itslef. If the game forgets to load a sound bank or load a wrong one because of a programming error, then playing song will sound different.
Apparently version 1 of this song is played with the BGM052.EMI soundbank, version 2 with BGM067.EMI, and I'm not sure about version 3 (pehaps BGM023.EMI ?).
If anyone knowns better than I
*) Where the music data itself is stored. There is non-sample data at the start of EMI files, but I'm not sure if this is music data or simply some kind of header for the soundbank itself.
*) If this music is stored multiple times or only one time
*) If the loading of the same song with different EMI is intentional or not
Just "guessing" it's intentional is not enough, sorry
Unfortunately I'm not very knowledgeable about PS1 reverse-engineering, so that's as far as I can go.
And yeah the soundtrack is pretty lacking, but clearly not as much as BOF2. There is still aprox. 100 pieces of music technically, and this song is here only once in the sountrack (in it's form of version 2).