[Edi]

It's not quite that simple. Sites are assigned in a game during the game creation phase BEFORE any map file specific instructions are applied. What this means is that unless the map file instructions for a given province do not include #killfeatures, randomly generated sites are applied first and scripted sites will only appear if there are enough free slots in the province.

If the map file has #killfeatures for a province, only scripted sites can ever appear there, since #killfeatures wipes out all the randomly generated sites.