im just saying you have everything u need to do it, also u wouldnt need to control the base just re-edit a planet with the model and have the ships warp in (in rebellion the tec rebels can call them in with the broadcasting tower , costs 5000-6000 credits) just have them do it for free and change the time from 600 seconds to every pirate raid along with the larger the bounty the more ships show up with of course being allied with the pirates already their and militia. only thing that would need to be added who be the capture ship buff so pirate could colonize.
The only thing is that you'd need to do custom maps to actually start at a pirate base planet. The normal maps will always have you start at terrans or deserts, but its easy to make those with Galaxy Forge.
There have been other mods that let you play with versions of the pirates in the past. None have been kept up to date with Rebellion. Zombie's Rouge faction has basically what you want I think, and more if you have Diplomacy.
Otherwise, sounds like a good place to start modding yourself. 
