Regarding the Penthouses on the HQ planets:
it’s intentional. They do count to the limits and the Pirate HQ planet always counted towards the PvE check.
It’s a decision a Pirate needs to make… either stay easy mode PvE or go full PvP mode.
Regarding Supergates see here:
The HQ Supergates are still not finished. I have something planned something special with them but no time yet.