Indeed the Nebula design and Miranda designs are definitely not systematic and not relative to registry, however in those cases it seems pretty conclusive that those variants are the result of specialized mission purposes which would justify different senor pods and weapons etc. The only exception was the Honshu subclass which exists because whoever made the Nebula CGI for First Contact (supposedly) used a Galaxy template to make the render thus looking different. And it's logical that the Lakota refit (again for specialized purpose) had been more prevalent in Starfleet we just only saw one onscreen in DS9. On that note if the Ambassador class had made it onscreen in Generations it would have had even lower warp engines than seen in the series and thus another variant. Eep!
Again it's a question that points to the intent of the design team at TNG what the cowl on the bussards and other changes were supposed to represent. Either way I do appreciate the input. It's fun to ponder this stuff although I'm still not sure what the answer could be lol.