As usual, you’ve missed the point. I’m not a biologist, and I’m not interested in going down a rabbit hole on your pet topic. But I graciously provided a link in the general direction anyway. Conceptually, prokaryotes are more analogous to the nuclei of eukaryote cells rather than entirely different in the manner you claim, though it is more complex than that. There’s no reason why I or anyone on this forum should be expected to know the answers to the questions you raise about complex biology, and it remains an argument from ignorance. At the end of it, you’re still no closer to any evidence for even a starting point for belief in a magical deity (also a false dichotomy).
Vastly complicating this problem for atheists
If you imagine any of this is a ‘problem for atheists’, you are very confused about what ‘atheist’ means. If you have questions about biology, ask a biologist.