I've made almost the same observations when considering the ships and the flavors we have with the factions so far Gilder.
I would also understand if some of the ships had been created in one location, than adapted dramatically to suit a similar but limited required role for another faction. Like the Junker, which you noted as modular, may have it's origins from Yesha but found popularity abroad as a support ship for several factions, each tacking on their own flare and flavors.