I'm not sure what all you are going on about but a couple of things... "Clone" in regards to mame is not the same definition as it normally is in life. You could have 2 versions of a game with different options and modes and mame would call them "clones". Many people don't like the term but it is what it is. There is the same problem with mame's use of "parent" when so many people think Japan versions should be the parent if the game originated there or the first version instead of most recent.
Anyway, the game data for CPS3 games is on the disc. The cart just tells it a security pass and where to point to on the disc - hispanic section, english section, japan, whatever. We can fake the cart data now to make all the missing regions but nobody who knows how to do it has done it because it is very boring work and lots of it. So the version you played before was some specific combination of region and cd revision that made the game the way you remember. You simply have to load it that way in mame, which might entail having to make a fake cart dump image for region and load that alongside the cd image revision you played.
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