Also, it would be quite often that a colony would be founded to exploit local resources, even if that means just arable land. Resource-rich worlds are a dime in a dozen in Trek as such. But by introducing the exploitation infrastructure and manpower, the colony would make itself more attractive to trade than to takeover and enslavement. Occupation takes resources, after all, whereas the colony could sell at very low price because it wouldn't really need the income, it'd be buying indirect protection through selling.
Selling to the commercial and hopefully not entirely state-controlled interests of a powerful empire might be a good compromise in that the empire would have little incentive to come and dictate policies (unless the resource were absolutely critical), yet a lot of incentive to perform all sorts of general maneuvers that keep competitors away from the resource. The agrarian worlds commonly seen would be good sources of non-critical goods that could be competitively offered without inconveniencing the colony itself much.
The Federation would be a good trading partner in that respect: a chain of independent colonies could be feeding an inner chain of UFP worlds out there where the central government would have logistical difficulties.
OTOH, the pumping station of ENT "Marauders" would be trading in a resource too crucial to avoid the attention of "control freak" customers, and the business would be too small potatoes to be able to play customers against each other... Something like that could only be run safely if deeply within a single customer's protective sphere, and that wouldn't give much leverage for maintaining independence.
Timo Saloniemi