I really don't have an answer to your question but maybe a suggestion. Our situations are different and unique to us. I have large flocks with several coops and can only tell you what has worked for me. Once in a great while I might find an egg on the floor of a coop or out in a pen but mostly in the nest boxes. My suggestion is to put something across the front along the bottom of the nest boxes. Mine aren't that low, probably like your top boxes. How many birds do you have? You only need 1 nest box for every 4/5 birds. I have had a dozen eggs before in one nest box and this coop has a dozen nest boxes. I have many coops that have 4 nest boxes in with around 20 birds in each but I don't usually get 20 eggs per day. Usually someone takes a day off, I have a way that I can add nest boxes as needed. Depending on the number of birds, maybe block off the bottom boxes and put something in front along the bottom of the upper boxes. The birds won't have a problem getting in and out of them and the nesting materials might stay in a little longer. I have golf balls in my nest boxes. They can't tell the difference. My hubby originally put roosts in front of the original nest boxes. I cut them off because that I think encouraged them to sleep on the nest box roosts, sometimes in the nest boxes and poop in them. No more. The single wood nest box (W/Buff Orpington?) in a picture, looks like it has a piece of wood across the bottom of the front of it. Good luck and have fun...