[Suicide Junkie]

The space yard ship shortcut to colonization is an irritant. I'll have to do something about that, and probably the asteroid mining base thing, at least for future Versions. I have a feeling people would get peeved if I changed it for existing PBW games... or at least, perhaps I can get feedback from players of existing PBW players on what if anything I should do to reduce the effectiveness of these techniques in existing games.

If you set the organics build rate on spaceborne yards to zero, then you could control which vehicles and objects require planetary support for say, crews.
Sats, mines, drones, retrofits and repairs can all be done, no problem. For fighters, only fully automated ones could be built.
(Make master computers use no organics, and possibly add a computer component for fighters)

You could have base-only yards that construct with organics, but require organics to build in the first place.
Call 'em "Full SpaceYard" and "Remote Spaceyard"

That way, orbital (full) yards would work normally, but you still can't build a full yard over an uncolonized planet...

In order to make absolutely sure people can't build a remote yard and then retrofit to a full yard, force them to be on different hulls. You could have the abilities built into 100kt copies of the Space Yard, (accounting for the 400kt of space saved).
Remove the components from available tech, so they can't be retrofitted onto regular bases.