I feel like they were SO CLOSE to things making relative sense in FO4. It's established that the Institute went west and found out about the Enclave (that's how they have super mutants, they got the FEV from the remnants of Mariposa instead of just having another completely different program to create the same virus like in FO3) and there's plenty of stuff that points to the commonwealth being such a shithole is because of a deliberate program of destabilization. The obvious conclusion to come to is that the Instituted has deliberately released mutants and infiltrated with synths in order to prevent the formation of an NCR equivalent, which would wipe them out.

Except then you infiltrate the Institute, and it turns none of that shit was planned, the super mutants got unleashed by mistake, and they're not infiltrating with any purpose other than making better synths and seeing what happens.