It's my understanding that the major factions do not manufacture the ships themselves, rather they are built and distributed by the various big Corporations (Gutamaya, Faulcon DeLacy etc). Although some Corps will have a closer relationship to some factions than others (Empire subsidise the design & manufacture of the Clipper?), there is still a more or less open market for them (I think you can get the Clipper without the prerequisite Empire Ranks by having a good Rep). This explains why Federal Generals can be found flying in Imperial Clippers, as they have the wealth and influence to pull strings (think North Korean officials still getting at western luxuries).