Breaking the Enclave IV into an Enclave V that works as the Enclave IV currently does and an Enclave IV that works like an Enclave III with better drones if there is no Advance Factory or a current Enclave IV if there is one doesn't make the Enclave IV more worthwhile to me. It makes Enclave IVs cheaper, but the main reason that I go into the Enclave line is for the mobile Advanced Factory anyways, and having the extra Mark V version costs me additional energy if I decide that I might as well use everything I spent knowledge unlocking (which, for full caps of all current Enclave Starships, is already 180,000 energy; with the current energy scaling on Enclave Starships, a single Mark V enclave would cost an additional 35,000 energy, so you're looking at almost two planets worth of energy to field caps of five marks of Enclave Starships, before considering any costs associated with drones).
I have also never found the Enclave drones to be worth enough to make Enclaves worthwhile independent of their use as mobile factories. If the only reason I have for unlocking Enclave IVs is to get Drone IVs, I'd rather spend the knowledge on something that I've had more use for in the past, like additional combat starships or more fleet ships or more turrets. Drones aren't bad, but when powering their mothership costs me as much energy as three combat starships or a cap of average fleet ships, I'd sooner have the combat starships or fleet ships, particularly when the mothership doesn't do anything that its lower-mark (and more energy-efficient) predecessor didn't.
I suppose it might be helpful to have the extra enclaves for faster fleet rebuilds, but I usually find that I can't produce ships out of more than two spacedocks without bankrupting myself anyways (unless I'm playing Fallen Spire, and even then it depends on how far I've gone with it), and I don't imagine it would be different for Enclaves.