i think that it would be better if you could beat her on the third time.
But the team eventually become stronger than her because they get through lots of travelling and battles:fencing: Meanwhile beatrix is hardly in combat becuase Brahne believes that its easier to use the black mages. I think that at the start of disc 3 most of your characters are stronger than beatrix.(not statistically because some people dont level up at all) i mean within the story of what the characters have been through

They manage to beat kuja becuase they all work together. four characters have to give the others the rest of their power for the final battle plus they had the spirit and will