My own preference would be for the presence of a fort to override any custom battlemap when there is a siege battle. As things are, we can't mod the forts anyway, so I see no need in custom fort battlemaps. Even if you wanted to modify the fort map, the initial battle for the province would take place in your custom fort map and then again when you try to storm the fort.
It may be that the structure of the code prevents an easy fix, but I guess there is no harm in asking.
