The problem is, the two colonies hold populations of different races, with different requirements in terms of habitability. As each colony can only have ONE colony cost, having several races in a single colony is a no-go.
This even applies, if you play a multi empire game with all empires of the same race (and also will apply, once you go the gen-modification route for your own race).
Also, the freshly conquered population realy doesn´t like you right now, so they basicly only work at gunpoint, leading to horrible efficiency (expressed in the "Political Status Production Modifyer, F2, lower right). And again, a colony can only have ONE of those modifiers and different populations have therefore to be kept in different colonies.
If you want to take over the buildings of the conquered race, you have to SM them in to your colony and delete them from the conquered one.