Zentor, you do fine work, and I love the freshness this will bring to the mod! Keep on rocking it, man!
With that said, a couple of words of friendly advice / caution. I know I promised to write up something ages ago, but better late than never, eh.
POB deployment
Please, be very careful with making POBs easily spammable. Yes, the current deployment system was a bit of a chore and needed some running around each time you wanted to set up a new base, but it was also quite a decent way to ensure not too many bases are spammed in too short of a time / too small of a space.
It's always awkward finding out a how a feature that was supposed to do good gets turned onto its' head by the more notorious members of the community.
About refineries...
The idea of refineries as they are currently implemented seems quite interesting, but I'd also be vary of making the refining process take just the raw ore, as this could lead to more mass mining and giant clouds of floaty ores, which we also know are not a good thing for the server.
A good compromise would be to have the recipes take one common, more expensive commodity that ensures the base can function normally (such as fuel) and one relatively cheap good that can act as a sort of "catalyst", that would be slowly consumed by the refining process.
This would ensure that the miners don't need to just repetitively run the field to storage base route, but they'd have to periodically switch to hauling the ore away and bringing in new fuel and new materials needed for the refining to work, thus clearing up all the leftover floating ores.
It would also offer an interesting tactical choice, do you keep your refinery going to get more credits and risk running out of fuel, and thus shielding for the base itself? Or do you stop the factory until the crisis is over ?
Crime doesn't pay... or does it ?
As for the "shady" side of POB business. Instead of a back room storage with the good stuff, think more about designing an actual unlawful economy that would focus on having refineries and factories for the "unlawful ores" (space weed farm or space meth lab, anyone ? ).
The unlawful factories would need to work the opposite way compared to ore refining, instead of decreasing the amount of commodities produced by the refining you would increase it. Think of drug dealers mixing flour and baking powder into the blow to make a small amount more profitable to sell.
Meaning the closer you build your unlawful refinery to the sell point, the more profitable it will be. But also more likely to get discovered by lawful patrols, and more chance for the law to intercept you or shut your place down, as you'd be making the run between the POB and the planet a lot. At the same time you'd go for the long haul to get your primary commodities from far away places just occasionally.
This would of course need to be balanced by having the setup costs for such an unlawful factory significantly higher, a risky business, some would say, but with great potential profits.
Whereas you'd build your ore refinery as close to the mining zone as possible, which would of course increase the chance of you getting pirated while mining / hauling stuff to or away from the base.
An actual unlawful economy would be a boon for all the police and intel factions to go around snooping for possible perpetrators that built an illegal factory on their installation. And also the Military factions that would finally get to use their big guns in sieges for gameplay reasons, not just OORP hate.