When I take over planets with buildings I can't use or shouldn't be able to use, they get "removed".
However, it would seem that some building that should fit into this paradigm, simply are not included. Examples:
Hyperian Logistics Blah
Miniturization building Blah..
Capitals (economic, political, manufacturing, etc...)
Some of these building have a significant impact on the game (like the +6 logistics building, or the +25% mini one) and some much less so (manufacturing, economic etc capitals)
Seems like a bug to me.. (or else you end up with incredibly powerful, normally unattainable fleets/combos)