I wish this had been addressed, but I feel like it would be easy to see Fleet Formation as a response to both the PRO and LD incidents. If you have a ship that’s compromised (like the Protostar or one of the Texas class ships), Fleet Formation lets you immediately deprive that ship (or any other infected ships) of autonomy by locking it into a unidirectional control from Starbase One. If it really can override anything else, that would mean that in the event of a Living Construct or whatever, Starfleet could just lock everything in Fleet Formation and the ending of PRO would never happen. But I guess they didn’t anticipate a threat coming from inside Starfleet.