How does the position of the seat make you see better in the dark? Do you walk into doors that are left closed as well?
She is referring to the relative circumference of the bowl, which is wider (and a lot colder) than the seat, and the female butt, which, at least when marriage is young, is generally smaller than the man's and therefore will slip down into the bowl if she tries to just sit down in the dark and the seat has been left up.
Someone else on here suggested turning on the light. If you are not a heavy sleeper, this would be enough to disrupt your ability to get back to sleep at all, and combined with the shock of the cold bowl rim and/or cold water, is a most unpleasant experience in the middle of the night.