What exactly he is doing is a little uncertain but Alan has said that he sometimes goes afk so that the stick figures can have a little fun.

I think he said in a QnA that he (in-universe) uses a different PC, than what the stick figures are on, because they are distracting and cause chaos all the time.

And yeah, he is totally right in thinking that.

I mean, the entirety of season three canonically took under 1.5 hours, so Alan could've just not been on at the time.

Well, alexcrafter28 was, so he couldn't have been asleep. He's an animator, so he couldn't have been working at that time, at least not at ALANSPC.

Why can't he be asleep? For one, timezones exist, and for another, alexcrafter might be a regular gamer and not have a sleep schedule.

Well, he was away the second time...just saying.

It took King Orange nearly 2 hours to destroy Minecraft. That staff is overpowered; I'm glad it's gone.