If the FO was in the flight deck and made the last radio transmission but then didn't re-establish comms with the next ATC, and with systems shutting down 2 minutes after that, I'm thinking it is highly likely he was in the flight deck. It seems unusual to decide to go for a bathroom break or similar at that short time between the radio calls.
Also, if there's any night you don't want the Captain paying too close attention, that was a good night. We know he had a long, stressful day(s) and no doubt had the day's events heavily on his mind. I wouldn't be surprised if the Captain was already resting in the cabin when things started to go wrong.
I'd like to know more about the FO...did he have any associates / friends onboard? Were they in the flight deck with him? Maybe he even had a simulator at home too. Lots of focus seems to be on the Captain but something isn't adding up with the FO either.