Since there are no rules listed for this game, I'm just copying the other runs for now, but I really think time should end when closing the cube holder thingy at the end of Death of the Firstborn. Unless you have the Owl Mask, you lose control over anything at that point. (Less importantly, I think time could start when the words, "The First Plague" appear, which is when the first playable screen loads, after you stop rowing the rowboat.)

Not trying to make it easier for myself to get ahead of everyone else (these rules would apply to all new runs), I just see things like this being done on other games. If nothing you do within those periods improves or worsens your time, why count them? (I've also noticed what I think might be some lag on my laptop during the flames in the final cutscene, which is minimal but ideally not something which should affect time.)