The at will protect from flap overspeed and vmo while and when you decide to retract the flaps when windshear is clear.
Whether you're flying manually or have the A/P engaged. So why leave it engaged with A/P but not when manually flying?
The reason is that the AT get info from many sources to produce the max thrust(via ADIRUS/EEC) and disconnecting it would not achieve the initial goal to get the max optimum thrust.
Max N1 is max N1, whether it's the A/T moving the thrust levers or the pilot. The EECs are the things that give you max thrust and will prevent you over-boosting (thrusting) the engines, not the A/T, so your statement does not make sense.
Bet you wish you'd never accused me of being a flight simmer
