While yes, I don't doubt that Bruce has the intellect to potentially replicate the Orthogonal Diagonalizer and all that other crap that happened in Godzilla Singular Point, the thing that irks me about the whole thing is that Godzilla (or at least the entity puppeteering him) purposely lost. It not only allowed itself to be defeated, it actively helped humanity to kill its avatar (on more than one occasion I may add). Without that help, I don't think that anything Hulk or Bruce have the means to kill Godzilla permanently because the entity is unreachable to them, the avatar can just ignore any attacks and pretend that they never happened in the first place by disconnecting cause from effect (as it does so multiple times in the novel), or even if they do kill an avatar, the entity can just spawn another one no problem. It should have been a draw honestly, because even if Ultima also lacks the means to permanently kill Hulk due to the Green Door or The One Below All or whatever, he or banner will never ever kill Ultima.