I would guess that automated systems (especially jettisoning storage) would not be implemented as the gain is to low for the risk in case of a false alarm. There would always be someone reachable and awake in case of emergency to close hatches manually. Warming up the landing module could be interesting though…

I hope the expert will answer!

Nope, 2 completely separate things. The only thing that was messed up in this case were the comm loops that were broadcast and maybe some of the simulated messages that are sometimes shown on one of the big screens in the room (that the sim was in, there are a few FCR’s (Flight Control Rooms)) - but I’m not sure if they showed anything visually from the sim. When you go to log on to an activity in MCC, you log on to the sim if you’re the one doing the sim. It’s a whole separate thing to log into the actual flight even though all of the computers are still in MCC to make the environment more realistic.

Edit: I completely misread this, lol, but no. The crew would close hatches if they needed to - there have been plenty of false smoke/fire alarms on ISS to wake them up while they were sleeping to troubleshoot. (One Shuttle flight in particular, I can’t remember which one, but it was docked, was particularly annoying wrt the ISS false detector alarms during sleep) and they were woken up and had to perform that emergency procedure. There is a lot that can be commanded from the ground, so it’s not “automated” in the way that you’re thinking. The ground has to send a command before anything happens. But closing hatches and such is done manually by the crew.