Other than the roosting issue, the height of the nesting boxes does not matter that much. Some people have them on the ground and some have them much higher. They all work though the chickens may get used to one situation and ignore new ones you add. Though when I added a new one, they all wanted to lay in it instead of the old ones. Trendy chickens that wanted the latest model, I guess.
A few things to consider. If you put them on the floor, they are more likely to scratch stuff in there from the coop floor. That may mean dirty eggs. Lots of people do it that way though and don't have that problem.
If you raise them just a bit but not enough, the area under the nests is a great place for Mommy Mouse to raise her babies. If the chickens can get to them, that won't happen. If you don't raise them enough, (considering the top of you bedding, not the bare floor) they will quite likely scratch the bedding and pile it up under the nests, blocking access underneath. Mne scratch a lot more around the feeder than under the nests.
If you have a bad back, you may not want to bend over and get the eggs out of a nest on the floor. Make them convenient for you. The chickens work for you, not the other way around. At least around here they do.
If you do put the nests directly under the roosts with a droppings board on top, make sure you can access the nests without your hair hitting the poopy roosts or the droppings board.
And don't forget the "roost on the highest thing" issue.