Sky Versus Sea: Fight!

Question: Do you think the episode of Set, Nepthys and the sea could be played as a conflict between Set and Poseidon?

I think that if you have a fun plot you want to spin off of that, sure, go for it. Egyptian mythology really doesn't have a sea-god thanks to their focus being narrowed down mostly to the Nile and surrounding environs, so there's no easy Egyptian figure to attach to the myth and the personified sea is merely itself. There is also no hint of any Greek influence in that particular myth, but Poseidon is the Greek god of the Mediterranean, and if you wanted to play it as an ancient political grudge-match kind of thing, you probably could.

Interestingly, I've seen scholarly suggestion that that particular myth might be heavily influenced by Canaanite mythology; in an alternate version, Set is instead married to Astarte (who was given to him as a sort of consolation prize after he lost the throne to Horus) and it's her he's saving from the ocean, which therefore probably refers to Yam, the Canaanite sea-god who's always startin' shit. This is probably a result of the fact that Egyptian and Canaanite territories overlapped and that Set and Baal, being both bad-tempered storm gods, might have been slightly conflated or worshiped together by some Egyptians in that area. If you wanted to, you could probably consider it a purely Canaanite myth and decide that it's referring to Baal, not Set, when it talks about going out to fight the sea.

Either way, though, the sea, whoever he is, is going to take a serious pounding to the face if he keeps these shenanigans up.