Tsk tsk tsk...you don't know a real torture story until you've played Persona. The original Persona (I think the PSP made slight changes that improve upon the system, but my pathological fear of the game makes me unable to prove that).
FFII isn't a bad game, much less based on its system. I'd speak of that since I've played several SaGa games, and I've enjoyed each of them. The one I've least enjoyed is...well, you'll probably figure it's Unlimited Saga, and it's the only game that doesn't have the tried-and-true system.
Considered how many hits you really landed? If you've defeated it on 3-4 rounds, considering the 2nd rationale, you've landed approximately 4000 (from the Masamune) + damage from Cat Claws (although I presume that's added into the 1000, so it can be obviated) + ((100-200) * 3 characters * 4 rounds) (which would be around 1200-2400). By the second rationale, you would've dealt 6,400 HP as maximum, which is not even half of his HP.
I'd add the fourth rationale of "it behaves like Zeromus", which originally was guessed to have over 64,000 HP but it was found that Zeromus recovers HP at apparently random intervals, so it seems to have more HP than before. Perhaps this is the case of the Emperor, which would imply the first rationale but with a corollary: it has less than 15,000 HP but the healing ability causes it to have an artificially higher amount of HP. If the HP count is based on the Bestiary though, it may perhaps be a throw-off from the game?
Also...usually, Petrify and Death are considered separate elements. Not sure if this applies on FFII, but is there a chance that you have a weapon that causes Petrify (that you know of) and that was equipped with some of your characters? Unless Petrify is considered as "Matter", it sounds reasonable.
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