TiLT - As I mentioned, you can run the many endeavors you need for upgrades as background endeavors. The book has a specific subsection on oursourcing parts of the 'Colony Endeavor', not the subsequent upgrades. Those would be covered by the normal Background Endeavor rules from Into the Storm. Unfortunately, they are less likely to succeed and can have negative consequences beyond simply not getting the infastructure you need. The colony does get a +10 on your check to see if the Background Endeavor succeeds if the colony leader is managing it though. Note that this is one way to make use of your colony leadership benifits outside of the colony as long as the colony leader could reasonable oversee them. For instance, establishing other endeavors in the system (such as asteroid mining, minor research, or even mines that aren't actually part of the colony) to generate PF.
The limits on harvesting resources are a reasonable roleplaying limtiation that I would provide to my players as a way to setting a fair expectation of what they can get away with without risking their control of the colony. You will note that they did not provide a specific roll required, simply 'convince their lackeys that this was all for the best.' To this GM, that means a series of social tests and some roleplaying. In order to do these tests 'they must put in an appearance at their colony' as well. As GM I would make it relatively easy to convince the colony once a year to provide such a tribute, but have the difficulty raise itself every subsequent attempt as the people get more and more disgruntled with having their efforts and resources taken without getting anything back. As a GM, I try to give the players a fair idea of what they can accomplish (and how much risk they have of failure) up front. You will note that the Imperium has had more than a few cases of rebellion over working conditions and poor treatment.
The way the system is written, the players have to at their colony every 90 days and convince the colonists to hand over the majority of the fruits of their labors in stripmining (and it it stripmining, as even a small colony can deplete a plentiful resource in a few years) their world and be happy about it. They must 'put in an appearance at their colony', they can not delegate this responsibility or run it by astropath. If they fail to convince the colony, the colony's Complacency decreases by 1d5. Note that 0 Comlacency will probably destroy a small colony (-1d5 Order/Productivity until you raise Complacency again, and 0 Order means complete anarchy and NO PF as your colony kills itself off 1 size per 90 days). So while you could just tell them to hand over the resources and suck it up, they would probably try to poison you and you would lose all the work you have put into the colony in quick order. The rules for colonies can be pretty unforgiving, as any time a stat drops to 0 you are in danger of the colony cascading into oblivion. Also, raising Complacency requires a Lesser Endeavor to install some sort of upgrade. So every time you fail to convince your colony you need to run 1d5 Lesser Endeavors to make up for the loss of Complacency. Note that you do not get PF for them, and that you are limited to a number of Support Upgrades equal to the colony size. Even failing to convince them two or three times could cause irrevovable damage to the colony. It is because the consequences of failure in this are so severe that I provide the players with a guideline of what they can expect to do reasonably safely. The colony should be profitable over the long term, but expecting to pull 3 PF every 90 days out of the colony immediately on founding (and for many years) seems excessive. What motivation is there to do anything else if you can just stripmine a colony for a few years and earn 60+ PF (on top of the base colony PF)?