I getting the suggestion here that a registered civilian vessel might be registered with "S.S." and no "NCC" (maybe "NAR" if we go by TNG references), whereas a true Starfleet ship would be registered with "U.S.S." and "NCC." The USS vessels apparently have some kind of jurisdiction over the others if we go by the "Mudd's Women" example. Following this through to Merrick, he might have a rank, but not a Starfleet rank, in the merchant service. Thank rank could be Captain or anything else appropriate. Starfleet as a "combined service" starts to make more sense in this context. Various jobs like exploring, patrolling, and defending are combined in this single service (with blue, green and red shirts respectively), while the Merchant Marine and/or independent scouts conduct most of what we would call economic business and prospecting, mining, trade and so on. To push this line of thinking further to answer another question, then the show could could call a "starship," anything that explores, patrols, or defends for Starfleet," while the others are called only "spaceships."