all "minor" factions should use civilian ships. only very few factions should be able to deploy their own ship designs. - in that case i am at a loss why the liberty rogues were given their own designs in the original content.
but most others - bundschuh, unioners, farmer alliance, gaians, in a way zoners use civilians, cause these ships are brilliant ( from their point of view ), they are unobtrusive - can most of all, can be maintained pretty much everywhere by everyone.
think of it... if you could only repair and resupply your ship at places that were possible for that ship ( roleplaywise ) people would like civilian vessels much more. ( like, if you would only repair, refit, restock an outcast ship at an outcast base, or a corsair ship at a corair base ... but a civilian ship at all cooperation, police and navy bases.. )
The mollies build the ships that the rogues use...I think we can agree that the mollies are a major faction, having been able to fend off the Baf in an open war.