If para-magic has scientific explanation and it is derived from magic then magic has scientific explanation on FF8.Even though they werenīt the same thing.
Not quite. The only explanation FFVIII gives for magic itself, not para-magic, is that it comes from Hyne--and even that isn't confirmed as anything more than a legend. Magic is left to be mysterious.

...but, even if it weren't, I don't see how it would help your point. Magic being explainable wouldn't lessen its power; there's still no reason to think that Ultimecia's castle isn't the way it is because she made it that way herself, unless I've missed something.