I'm happy with the notion that the two variants may even have been produced simultaneously. Today, we have several variants of cars, airliners, and even naval warships being produced at the same time. Normally this is because of slightly different mission requirements: for nor example, a Boeing 737-600 series is shorter than an -800 and carries less passengers, but makes more economic sense for flights of a certain duration on routes that see so many paying people.
It's entirely possible that the variant carries out a slightly different mission than the original, or is equipped to do so. We similarly know that the Excelsior and her variants were produced concurrently, with some batches sporting the extra bulges while later vessels lack them. Who knows what these changes are - more cargo space for some, an extra shuttle bay?
Maybe it's like today's Airbus A380, which comes in two versions depending on which engine the airline chooses. This could also be an example of that - Ambassadors meant for deep space exploration missions would have slightly different engines optimized for long duration warp, plus an extra shuttle or cargo bay for the additional stuff they'd be taking with them. Fifty years after construction, those ships would still maintain those variations regardless of what mission they were actually assigned to...