What's also strange is that normally when you colonize a new planet, you only see the standard buildings (f.i basic factory) and it automatically upgrades to more, if you have researched the proper tech and your que is empty.
But when you conquer planets, you also suddenly see upgrades there like manufacturing centres you can choose to build. And indeed the mentioned special buildings.
Also it is still possible to build a secondary planetary defense system, after you build an initial one which was later upgraded to the planetary defense dome (PS the picture for the planetary defense dome is the same as the one for quantum power plant, just a slightly different color..don't know if that is intentional or just a temporary solution?)
