They are not gods, they are just intelligences that have appeared naturally. I would also say they don't have free will because free will is an impossibility, but we will lieve that for another discussion.

Science does not pretend to be able to understand everything. It is normal that at a certain point we are unable to observe various phenomena and so we are unable to create theories. So one shouldn't be surprised if at some point science reaches its limits, and one should refrain from using the god of the gaps explanation when that happens.

I don't see why you reject the idea of a multiverse. If there is one universe, there could be 2 or a zillion. It is only a lack a imagination on your part. It is not pure philosophy, it is logic.

Would it be only philosophy to say that there are other continents, planets or galaxies if you only were able to observe the ones you are in? No, it would be logic, because you know that nature tends to create natural phenomena in very large numbers.