I believe the notching is indeed a big part of it. Notching a correct age larvae causes the bees to treat the larvae as a queen cell. By notching, the bees are better able to enlarge the worker cell into proper queen rearing size and don't have to waste royal jelly floating the larvae into a more commodious space. That enhances the larvae's nutrition and that is what it is all about.
At the bee college this past weekend, they talked about that and the fact that the queen larva cannot use the royal jelly that is also in the horizontal section of the cell. Like you said, it is just to float it out.
Also the cell that is open to the bottom tells the bees that that cell should bee a queen cell.