I agree with you that it was probably just emotion and adrenaline. And, Fedor was probably completely done before those two punches landed. The problem is that because of those two illegal shots, we don't know if Fedor was completely done or not.
How many fights have we seen lately where a fighter lands a perfect hook that clips the back of the head and drops the fighter, practically out cold, simply because of the placement? Because we know that shots to the back of the head can seriously mess with your equilibrium and consciousness, there is a problem when a rocked/dropped fighter is finished with illegal shots to the back of the head.
I don't think it would have mattered, since herb dean himself said he was stopping it when Fedor first dropped and the last two punches were just not factored in the stoppage. Fedor still would have lost even if Dan just got up at that point and did cartwheels.
In the gif, it looked like the first punched landed on the back of the head but the second seemed to hit in more behind the ear which I think is a legal shot (Although the definition for "back of the head" is well defined in MMA). Either way, Fedor was out before he hit the mat (according the the ref), so Henderson was the rightful winner.