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Listen I get the theorizing but there Gilgamesh is just one of many gods out there. I don’t think he’s a Greek god unless Mojito is referencing ore-hellenistic mythology (which is real possibility).
There a couple possibilities. I’d have to go back and re-read the chapter when FG was actually introduced (as an ally to Isis) but if it is a Greek god then I’m thinking Posideon. And if not then maybe something g like Abzu (Babylonian primordial deity that shares a very similar role). I think he’s associated with water (mainly because his introduction was in part related to the time Isis tried to just flood everything). If I recall he was a part of the plan.