Those small coops do have challenges, not always apparent ones. There is always a learning curve with any coop. Things usually don't work out exactly as you think they will or should. Personal preferences come into play too.
Your specific question was about using height so I'll use these photos. The top one is my built-in brooder under the main roosts. The top of the brooder acts as a droppings board. The other one shows my nests with a juvenile roost over them. This is a case where things did not work out as planned and I added a juvenile roost. Anyway the top of my nests act as a droppings board. as poorly designed as that is. To save space you might feed and water under your droppings board. Just some things to consider.
A droppings board should cover the area about 12" either side of your roosts and your roosts should be a minimum of 12" from your wall. In a small coop like yours that is a fair amount of space.
I agree with Aart, the higher the roosts the more clear landing area they need. In your place I would build two nests and keep them pretty low. Make your roost higher than anywhere you don't want then to sleep, such as your nests, but make them as low as reasonable.
My personal preference is to walk into the area where the chickens are to gather eggs, feed, and do all that. There can be legitimate reasons to collect the eggs from outside, but I'm going in to feed and water anyway. Plus I've found a few snakes, a dead chicken, and even once a live possum in here that I probably would not have found if I were not going inside.
One way to possibly save space, especially to allow you more room to work in there, would be to hang the nests external, on an outside wall. Build them strong so they are not an easy way for a predator to get in and you may have to gather them outside in bad weather. There are always trade-offs.
Personally I'd change your entrance/storage area to just a small storage area and have an L-shaped coop. To me that is a lot of wasted space. And I'd consider moving the doors over to the end of the wall instead of in the middle, I think that gives you more usable space. And pay close attention to door swing, like maybe swing out instead of in so you don't have to keep that area as clear.
I also like overhang. On the side walls I stop the wall panels a little short and cover that space with hardware cloth. The way my rafters run that makes installing the side panels easier anyway. I'd consider leaving an area over your front door open and covered with hardware cloth, but probably that is unnecessary. But on the back door, where it is going into the run and is totally covered by that roof I'd leave a big area open and cover it with hardware cloth. Great protected ventilation. As long as all those openings are well over their heads when they are on the roosts you should be in good shape.
I rarely get paper wasp nests in the coop. When I do I knock them down and let the chickens eat the larva in the nest. If the wasps fly down where the chickens can get them the chickens will eat them, or at least try.
Lots of personal preferences here. This is intended more to give you things to think about than trying to tell you how to do it. Good luck!