Hrm, spent some time on this, interesting results.
People who Threw Away the Will to Live
At first I thought the activate version was a problem related specifically to the 1000 AD music, for example, the old SPC not being fully cleared out of memory. BTW, I was using the piano man at the Snail Stop instead. Then I tried 65m BC. When you enter Laruba Ruins from the map, most of the time you get the ct-204.spc. But, if you keep entering and exiting, eventually you'll get the activate variant. You may need to wait a little bit on the overworld map before entering again, or Fast Forward the emulator.
I though maybe this was purely an emulator sound glitch. So, I dug out my SNES console, and it actually happens on there, too. In fact, there seems to be a third variant, unless I'm hearing things. It sounds closer to #1 (ct-204.spc), but slower, if that makes sense. Kind of the opposite of #2. Try it out, see if you can get all three versions from Laruba. No PAR cheats or anything are needed. Anyone else reading this thread, if you can confirm it as well, that would be great.
Why is it happening? I'm guessing it's just a little feature they added. Unless it's some bug in the game's sound engine or something. I wonder if any other songs are affected?
Final Battle
I hear the same differences, the one from the old set (I'll call it #1) is louder, and sounds better. Every .SPC capture I tried, however, gives the weaker newer version (#2)
If you mute the right speaker for #2, when the song begins (after the Lavos scream of course) you can hear a VERY clear volume drop. This doesn't happen with #1. But, listening to the song in the emulator (and again, on the actual SNES) it's very tough to say which SPC it matches more. I think I hear the volume drop, but not drastic like SPC #2. Overall, it sounds right between #1 and #2. Thoughts?