I like B for organelles and A for engulfing.
For B for engulfing, this would probably be much too easy to get very different types of organelles.
Perhaps a fusion, where there is a separate toggle but it isn’t guaranteed to give them the things they engulf as organelles.
Instead of editing endosymbiotes, I would like it if the endosymbiote was affected by auto-evo.
So for ones with flagella, auto-evo should get rid of it since it would be useless inside another cell.
And for ones with metabolosomes + a rusticyanin, if the player never collected iron, auto-evo would ideally get rid of it.
I like your idea for the way nuclei would work, except that a large mostly-cytoplasm (or is it protoplasm that prokaryotes use?) endosymbiote would turn into one, as I don’t think that is how they are proposed to have evolved. I am also not sure vacuoles arose from endosymbiotes; I think the organelles that are mainly accepted to have arisen from endosymbiotes are mitochondria and chloroplasts.
So the player would want to even have endosymbiotes because they would be either smaller or more efficient than just the proteins by themselves. And, of course, they could add a whole endosymbiote at once (probably for less MP) instead of having to place the proteins one by one.
So for acquiring vacuoles (and perhaps the nucleus, though I might prefer a slower transition requiring several generations), they could just be they same way they are now.