Can you be more specific?
From the ones I know (detailed in OP) and have been listening to for decades, they are just interpretations of the same PRELUDE work.
FINAL FANTASY PRELUDE / プレリュード as being the Press Start / New Game / Continue selection screen music (BGM) is meant to have a new recording for each game.
Same for the FINAL FANTASY MAIN THEME (heard in most ending titles).
When called FFXII Version for instance, we should understand it as a new recording, a new interpretation. Listen to it, it’s not a new work, it has same melody and chord progression.
That a new recording gets some new arrangements, I mean it’s what’s interesting with new recordings.
PRELUDE has those two versions, no doubt.
But the others.
Please be more specific (with links, maybe?) where the composer, the publisher, the gamers consider PRELUDE and THEME are many different works.