Evolution of Early Planets

I already mentioned something like this in the Discord a while ago, but I suppose it’s relevant to this thread so I’ll rehash it here. Sorry if it’s a bit of a mess, I’m mostly throwing random thoughts together at 3am so please bear with me

I had a few questions and concerns about how evolution works in response to events and such:

For instance, as oxygen levels rise due to photosynthesis, what’s stopping nearly every previously anaerobic cell from independently adapting metabolosomes? Oxygen is toxic to obligate anaerobes, so realistically you’d expect an oxidation event to weed out the vast majority of these species, save for those still in oxygen-poor areas and those who were lucky enough to evolve some way of dealing with the increased concentrations of oxygen, which iirc is what happened on Earth.

But according to my current understanding of how auto-evo will work, basically every cell, eukaryotes included, would end up evolving metabolosomes sooner or later because they’re easily available in a single generation and, in a world where the air is slowly killing you, are easily one of the best choices for avoiding extinction. Perhaps a few very unlucky species would go extinct, but the majority would survive.

Wouldn’t it make more sense if aerobic proteins are something that are only evolved once or maybe a few times, (including by the player for gameplay’s sake of course) that all aerobic cells would then be descended from? (partially including eukaryotes with mitochondria)
Weren’t eukaryotes anaerobic until mitochondria came along? I think oxygen-producing photosynthesis only really evolved once on Earth, in cyanobacteria, but what about aerobic respiration?

How do we lock the majority of species out of a certain adaptation without it feeling artificial or making it equally hard for the player?

I’d also like to bring up some things about endosymbiosis too.

How would an anaerobic eukaryote manage to even be in the same environment as an aerobic “proto-mitochondrion?” Wouldn’t the oxygen that the aerobic bacteria thrive on be toxic to the eukaryote? Or would it happen in some sort of in-between zone, where the oxygen is enough to maintain the populations of aerobic bacteria, but not enough to kill the anaerobes? Or would the anaerobes evolve some way to tolerate the oxygen? How would that work?

Also, if a eukaryote already has metabolosomes, what realistically is stopping it from adapting and specializing those metabolosomes until they’re as efficient as a mitochondria?
Would it make sense for mitochondria and such to start out as effective as one or two metabolosomes, and the player could specialize them and make them more efficient?

Would it be an interesting mechanic if, instead of unlocking “mitochondria” or “chloroplasts” based on what cells you engulf, you got the actual cell you engulfed and can place it in your cell as an organelle, and could modify and improve it?
What if you assimilate a cell that already has an endosymbiont?

Obviously stuff like this is pretty far into the future and we don’t really need to think about implementing any of it just yet, but it could be useful later on as we try to figure out how to accurately represent evolution.