Given the parameters you mentioned, it sounds like the decision is made either at the start of the game, or within the first few seconds.
I suggest you create a separate "new" base with its "new" object for each faction. Then use a single worldbuilder script to decide which base is to be the starting base for each faction based on the model condition of whatever object is deciding. The starting fortresses and porters might need to already be there, but that script would run once at the beginning of the game possibly deleting them and substituting the "new" bases. From then on, only the selected base would be built... wherever it is supposed to be.
You could avoid any jerky or sudden flickers of the starting fortresses and porters caused by the replacement of the starting base by having the camera looking somewhere else at the beginning of the game.. or maybe a very dark screen with some text describing how horrible the coming battle was going to be, then fading in the light.