Spoiler
If it weren't for this entry in the beta 4 changelog, I would have thought nothing of it, but:
FIX: Opening super secret hidden door with the proper manual code triggered the security system anyway [GJ]
This makes me think the security system is not supposed to activate if you have the code from Zhirov. Is that right? Or did I mess it up by checking the cloaking terminal by the door?
The log says "Scanners sweep the area" and as per the screenshot the miniboss showed up.
Nope this is working as intended. Opening the door itself with that code used to trigger a separate system, the one protecting the walls/doors from attack. The system inside is something else.