From what I've been able to poke around and see, also from my reading on Japanses message boards, I have found why the CT rom is there and also how the other SNES<->PSX work as well. In true halkun posting style I must, of courese, write a novel about everything else before getting to my point. ^_^
From what I gather, once unpon a time in Squarsoft, word come down on high that the SNES games made by Square would be put togeather ino a compiliation pack. This was done for two reasons, first profit (They *are* a company you know) and second, to get the game's source code into a more portable format. (The original games were written in a mix of assembly and Nintendo's object code)
Now the SNES can only handle 32K at a time, so roms were commaonly broken up into "banks" to be swapped in and out. Sound was handled by a totaly different CPU with it's own memory too. This result is many "Parts" to a SNES game.
FF4 was ported by breaking up the ROM into parts and having the core engine rewritten. FF1 is only 1 Megabyte so they were load the while thing into memory in a PSX and have room to spare for the engine (That's why it runs the quickest out of all the ports) FF4 was broken into two parts. "Battle", and for all intensive purposes "Field". Sound was removed and replaced by something that just plays back the prerecorded music, As opposed to being done "on the fly" Sound effects are also done this wat too. The Save system was scrapped and replaced too.
With FF5 they ran into a problem, it was 2.5 Meg and won't all fit onto the PSX memory. Square had to resort the the same "banking" technique that they used in the SNES. So the broke that up too. The sound and the save system was removed an replaced by more portable code (Still played pre-recorded music ans SFX) and now there was a modules for battle, field, overworld, and menu. That's why it takes so long to pull up a menu, it has to load the whole thing from the CD-ROM which takes time.
FF6 weighs in at 3 Meg. Too big for the PSX. That was broken apart. Sound and Saves, same deal, but now it was broken into many files to make banking much less a load pain.
When CT was released it was decided to be a stand-alone in Japan. It was decided to actully intagrate the video into the game. The rom was broken up and the actual ROM.BIN *supposed* be be a dummy file. (The dummy files on the other SNES ports are the roms too, but they were zeroed out during the burn process) it's a left over from the devopment cycle. Replacing it won't really do anything as is is not used. The localazation team probably could't get the licence from Nintendo to put the english rom in there (Remeber, american releases are licenced through the big N) so it was the Japanese rom stuck.
Wow, I wrote alot again... Oh well, you guys get it.