My impression is that the only problem the Enclave IV has is that most people aren't willing to spend the knowledge to unlock it in a normal game. There's nothing particularly unbalanced about it; rather, people are disappointed that there is this one really expensive ship that they never unlock because they don't have a use for replaceable Mk IV fleetship production facilities. In Fallen Spire campaigns, or exo-heavy games, Enclave IVs are almost the only way to retain access to Mk IV production, and at least in FS campaigns where you try to conquer a large empire the high knowledge cost is a relatively minor obstacle. Losing access to a replaceable Mk IV production facility is something I'd kind of regret, even though I don't use it very often. Not everything needs to be balanced for use in normal games, even if it's available in a normal game.
*Note that when I said "FS campaigns where you try to conquer a large empire" I meant "a large empire for an FS campaign".