[Fyron]

You can not directly modify the starting facilities. All you can do is mess around with the facilities and the tech tree. The starting facilities are determined by ability. For the resource, research and space yard ones, the one with the best ability of that type is placed on the HW. For the spaceport and resupply depot ones, I believe that the Last facility in the file with the respective ability that is available due to technology is placed on the HW.