The Machine was probably aware Samaritan was behind all the vote rigging. I'm guessing Samaritan wasn't exactly trying or bothering to cover its tracks from another supercomputer AI.

I might have missed or misunderstood something but didn't Root say the machine hadn't been talking to her directly? How did she activate her god mode then?

Had they just left Simon to die, the hotel receptionist wouldn't have died.

Hm, that was what I got out of it as well. He stepped down simply because he understood Harold's statement as a warning.

I wished they had zoomed out and shown the Machine's POV then. I always love those pull-out end-scenes, and this seemed like a perfect opportunity.

No, not a retcon at all. It was not stated outright (even in this episode, it wasn't stated outright) that it was an AI, but the very first creation flashback in season 2 pretty much established this. That whole flashback then was about Harold teaching the Machine to NOT care so much (i.e. don't focus solely on saving…