This is why time limits, I think, need to be tied to the difficulty mode. The AI being in danger of advancing past you should be a fun condition to try to combat against (and probably should be disabled entirely in easy mode).
The reason why I’m very against even trying to make the game work is exactly this:
It would be an absolute nightmare to design the game simulation, performance, and program being able to make this work in any other way than just declaring the game to be over.
If we put this into the game plans we are going to make each stage so much slower than if we just make the game an experience with a start and a finish and constrain the AI to playing the same stage as the player. BTW this is exactly the massive problem that a full multiplayer mode for Thrive would have (and there’s no easy solutions there either).
However a pretty key question is that could a new multicellular life branch evolve after many multicellular species already exist? If not then being a single cell when multicellular creatures are already prevalent would be a permanently locked to the microbe stage scenario, which at least needs a big popup telling the player that they can no longer ever beat the current save.