I personally think that the manager is an AI, created by someone, possibly from that group that's starting the TechUprising that the Admin at the end talked about. I don't know what to think of the blue mist, honestly. But I know it's connected to the system itself (why else would blue mist just pop up in your screen? Also, Manager 13 tries really hard to pass it off as normal fog.)
I think when someone's eliminated, they really are killed IRL. The Bluetooth thing in Noise Complaint/Intruder is probably part of Mind control?
Honestly, at this point, I'm inclined to trust Admin/Jensen. But we can't really say for sure, because we lack data about Manager 13, except that 1) he tries really hard to keep you happy in your job, going so far as to give you 5 stars and skills, 2) he has moments when he doesn't act like a person (repetitive phrases at the end before the glitch: 'you're doing a really good job' ) 3) when he does act like a person, it seems like there's someone monitoring him as he works so he can't just say 'Good Job [Name]. Go out there and Slay 'Em!' without getting blocked.