Wrathmonk,
Difficult answer and one I haven't really thought through but for starters a boss must be proficient on type and know the equipment inside out. Only in that way can you avoid nonsense tasking. We had one once where the aircraft performance data came from the Observer's Book of aircraft.
Also my initial captain was the Task Force Commander, a gp capt, although he handed over later to the copilot, a wg cdr. Now on that operation we could probably have managed as the tasking was unlikely to be more than a couple of sorties but if it had gone in to intensive ops things could have been quite tight with no exec on the ground.
So, logically, once the initial baptism of fire was passed, and the operations became more routine, then it would matter less if the CO flew and was diverted, in rest, or worse.
As an aircrew sqn cdr I think it probably esential that the boss is available to run the outfit during that all important transition from peace to war. Just when that transition changes to steady state is of course another question.