As I read the page I linked, the person inside the cockpit is able to override the override entry code. An unconscious person can't do that. An unconscious person also does not command a descent right after reaching cruise altitude. The simplest explanation is that the pilot or a burly flight attendant or attacker took control* and kept that door locked.

Edited to add:
*It would be fairly quick to program a descent, then leave the controls and stand next to the door to guard against entry.