TL;DR: Omnipotent beings in fiction aren’t omnipotent because their power extends only over the work they exist in.
Omnipotence is the state or ability of being able to do absolutely anything and everything whatsoever without drawbacks. For example, you could run and fly at the speed of light, lift infinitely heavy things, create and destroy absolutely anything; heck, you could manipulate even logic itself! You could be erased from existence and then just simply recreate yourself from literal non-existence. You could blink so apple-like that Santa in the Speedforce would cry chocolately about it like an elf in Magius. Does that make sense? Absolutely not, but that is omnipotence in essence.
So, in different fictional universes, omnipotent beings can exist. For example, the Presence in DC and the One Above All from Marvel are both omnipotent beings. However, I would argue that they (and every fictional “omnipotent” character for that matter) is actually not omnipotent. This is because omnipotence is the ability to do anything and everything; neither of them would be able to, say, stick their hand of the comic panel they’re in and pull you inside, nor can they affect anything in real life. If you were really omnipotent in real life, you’d be able to casually pull fictional comic and manga characters into real life the same way a magician could pull a rabbit out of their hat.
However, it’s a bit disputable whether omnipotent characters are omnipotent even within their own respective fictional universes, because of a paradox. Now, if you’re omnipotent, you could theoretically create a rock that not even you could lift. However, if not even you could lift it, then you’re, in actuality, not omnipotent. As such, the same could hypothetically apply to fictional omnipotent characters.
However, even if a character is truly 100% omnipotent, the writer is arguably infinitely more powerful than them, since they could always just say the protagonist can punch an omnipotent dude and win anyway because why not and simply leave it at that (or literally anything else).