If the Make Permanent box is checked, the corpse will never go away. The game can't remove it.
As for other non marked corpses, the counter starts when the cell is entered. But, this only affects corpses that are not marked permanent.
What would be an interesting experiment is to see if the mod would replace those unmarked corpses after 72 hours (after you reload the game once they are removed by the timer). Quite frankly, I don't see that happening, but I don't remember any cells that already had dead corpses in it when I entered, other than the perma corpses. So, it could be that the game will remove any corpse that is not marked permanent. Which is probably why they added that option to the NPCs.
You could do a quick experiment on the one in Hlaalu Council Hall. Make a mod that removes the check box, load up the game, visit the council house, then wait somewhere for 73 hours, then go back. It might take longer than that though. I would carry this out for 31 days before I called it good, or bad.