Yeah, that's why I feel like the issue can become a lot more complex than what the simple labels we attach to people in the different camps would suggest. A member of such a species that created the universe through natural means might meet the conception of what the religious call "god," but the irreligious wouldn't label them as such and would seek to understand where they came from and through what natural laws they went about creating, etc. rather than relying on faith in their wisdom in doing things.
I'm not following your reasoning about atheists not needing to disprove anything though. I think the empiric evidence is pretty scant in religious discussions, but I'm not sure I'd qualify the examples you gave (virgin birth, walking on water, water into wine and the like) as scientific impossibilities either. For example, parthenogenesis is interesting:
https://www.scientificamerican.com/article/strange-but-true-komodo-d/. This example doesn't represent any evidence that this has ever happened in humans or anything like that, it's more just to illustrate the point that something may be possible, we just don't understand how the act might work from a scientific standpoint. We need to rely on the scientific method to discover whether such a thing is possible. The point I'm really trying to make is, I think it can be a bit dishonest to say that believing such a thing is ridiculous because "current science says it's impossible" when further scientific inquiry might reveal a possibility that was not previously known.