The ability to build your own MK IV Factory notwithstanding?
Well yeah. The way you balance a game like this, especially with such a small playerbase (in comparison) is not to balance on what a ship
could do in the best possible hands - you balance based on what players are actually doing with it. It could be that parasites and siege starships have always been the most broken units in the game, but if nobody uses them or realizes it, that doesn't have a lot of value does it?
If nobody is using MKIV Neinzul Enclaves, then they probably need a buff until people use them. I know a lot of us use Core Shield Generators, so we might only use these if our Factory was taken out, or if we were using a heavy Neinzul strategy.
You have to factor in that the cost in knowledge of unlocking the Starship is basically 100 AIP. Even if you opted to skip the Factory planet (don't know why you would), this knowledge would probably be better-spent elsewhere. 14k knowledge is 2 and 1/3rd level III/IV units that you aren't going to get anyway. In its current state, I would much rather have beefed up defenses and/or extra starships than spend my knowledge on that, and I think most people feel the same.