I like it. This is the basic, but spelled-out version, of the ideas I've promoted in the past.
In order to bypass the whole "Ship docked to turret dock: What do?" thing, just add this requirement: If the object in question has a means of propulsion (Push pulse or thrusters, not jump drive), then it requires no crew from the mothership to be functional.
BOBBY AIs can stay, they just have to retain low-level AI functionality. Perhaps "Can control up to X mass, and up to Y system complexity" where system complexity is determined by a function relating number and size of systems to each other (Converting, say, 100 system blocks into the equivalent of 1 extra system, depending on config or whatever). So yes, you could, conceivably, still deploy ludicrous numbers of distractor drones...but they will cost your mothership. Crew could have the same complexity limits. So having 200 different ship cores docked to your ship is going to cost you, say, 100 crew members for maintenance (Because that 200 is added to ship complexity, which only needs to be recalculated when blocks are added. Heck, could have a 5 minute cooldown after last block added, so that 5 minutes after you finish building, it checks crew requirements, that way avoiding extra lag every time you place a block.