My outlook on this is that, you have the final boss, but he's meant to be "beatable" so that more players can experience the story.

But if you want the crazy extra challenge, insane min-maxing, greater rewards, and other stuff, you get ready to fight the Emerald Weapon, Omega Weapon, Death on the Clock Tower, Sephiroth in the Coliseum, etc.

edit: It almost feels like your post grew in length while I was typing this. I guess it depends on the type of scaling. And even then, might be harder to balance out, since would scaling only involve increased HP? Or would it increase the boss's stats, thus lowering the party's effectiveness, and making calculations across different level ranges even more difficult?