No one is going to be able to answer this, since:

A) The anthology version has the only official script.

B) It was never released outside Japan in any other form, so no one has ever played it on a SNES.

As far as I know though, the only differences are you can hold down the 'cancel' button in order to run, and the added FMV's.

I would just take the Anthology version as being the only real version, and leave it at that. There might be someone here who has the Japanese version, or knows all of the specific differences though…

It isn't like FFIV though, there is no 'hard' or 'easy' type of game.