I'm not entirely sure, but I think that the door was not ordinarily used by anyone, something akin to the jail version of a fire exit. I believe it was set to alarm regardless of who opened it, but if an authorized person opened it, presumably they would let whomever receives the alarms know about it in advance and not send in an army of officers.

Presumably they disable the alarms before the guards open the doors, and enable the alarms when the prisoners are unsupervised. Like how you enable your house alarm when you leave, and then disable it when you return home.