AI doesn't flee yet. The player's flee button is stub.
The current idea, that still needs to be tested: when you click the flee button, the game shows you a trigger that you have to reach. If you reach it, you successfully flee to the latest safe point you defined.
The AI would use the same: when they decide to flee, they'll have to reach a spot, and they'll be gone from the game (lost XP).
AI will only flee if they're dumb grunts, small cannon fodder that panics when they're outnumbered and their "chief" is dead for instance. Depends on their script. (Not all dumb grunts panic. Orcs smash.)
This works on paper, still have to see it in game (and break it).
When you are in TB and I am not, yes, you can hold on to your first turn until I arrive to come and help you.
When someone joins you in MP, you can set timeouts for their TB turns (and set it to "none").