“(But of course, neither is going to be the final boss.)” What makes you think that? And who are some other candidates?
I’m quite convinced the final boss of the story is going to be the apocalyptic threat Dinah predicted. Possibly a gargantuan worm of some kind?
I do suspect the remaining Endbringers might show up to make Brockton Bay (or wherever Skitter might move to if Brockton Bay is deemed unlivable) even more of a wreck before then, serving as bosses for the second and third parts of the story like Leviathan did for the first, though.
It’s just that I don’t think it will be over once the third boss (Behemoth, I think) is dealt with.