The 14k knowledge is not worth what the MKIV Enclave gives you, even with the drones.
If you just want to deep strike, you can do that just fine without spending a dime on Enclave Ships (I did it in my last game with the 2 MKI Enclaves and the Merc MKII, but there are tons of other deep-strike options as well).
If you just want to build MKIV ships, you can capture the factory and use Intergalactic Warpgates if necessary.
None of this would probably matter, except for the fact that Neinzul bonus ships, of the MKIV variety, are extremely situational and non-cost-effective if you are forced to spam them from a fixed point in the galaxy, or wait for them to come through the IG Warpgates.
In short, without changing some major game mechanic, separating the MKIV Enclave into 2 parts (a cheaper one that requires a Factory, an expensive one that doesn't), makes MKIV Neinzul ships very useful, without changing any core mechanics of the game.