Well, there's an "all clear" response from site command in SCP-076's containment site that shuts down it's security. I agree with Luna's idea, and now its time for... LOGIC
Logic time: People enter the site through the entrance zone, people need a level five keycard to enter the HCZ and the LCZ, because there is no way to access the LCZ without going through the HCZ. Only a few people have Level 5 clearance, and only a select few and members of Site Command have Level 4 clearance, so what your saying is, members of site command cannot go outside of the entrance zone. Another point, one can find level 1,2,3, and 4 cards inside the LCZ and HCZ. How did any person with that clearance even make it in the containment areas?
On your other point: Yes, as you can see by that inaccessible side room by the checkpoint doors, there is most likely a guard stationed there. If there is a keycard reader between the two doors, I think he is not the one to open and close the checkpoint doors, and he most certainly does not have level 5 clearance if that is what's required to open them. In conclusion, in canon, there is no way those doors can have such a high clearance level to open. It would most likely take level 2 or even level 1 to open. The need for a high level keycard must be placed somewhere else.