I just had a listen and while it's much better sequenced than the v1.0 of this patch, the orchestral opening is still off toward the end. I know that even the original GBA version got it wrong too, and while this is still preferable to how the vanilla GBA version did it, it's still jarring.
Yes, in the original SNES version there is this strong note when the cristal is explosing (which doesn't happen in the "vanilla" GBA version and also doesn't happen if you play the SNES original on a PAL SNES for example), but I never know if this synchronization was on purpose or if it was just some coincidence. That is because you know the intro is never entirely played in the SNES version, there is a good part of the song that will never be heard in the Boco / Barz scene (this also happens in the GBA "vanilla" version and in my verison), which makes me thing Uematsu composed the song as it and that they inserted it in the SNES game without thinking too much, and it just happened that the crystal exploded at the time this "strong note" plays.
I also wanted the orchestra to play at the exact time of the explosion of the cristal but it would have been hard to do, because a part of the intro is lacking in the orchestral version I had to slow it down to 80% of its tempo for this version (the version 1.0 didn't alter the tempo), but to have this note at the explosion of the cristal I'd had to slow it down even further to ~65%, and it would sound really slow but also create a lot of artifacts in the sounds, and then the Butz&Chocobo part would start too late so the end of the intro would have to be fastened, and it would sound even weirder so this is why I did it like it it.
Now I'm really glad some people appreciate the hack, which the first posts did make me thought of the opposite. I guess I just wasn't lucky with the first people to comment here.