Repeating myself, our old vet used to say that half his work was patching up horses their owners insisted were better off living with others to pick on and run from. 
OP, all of us prefer one or another type management and you are getting all kinds of opinions.
In the end, only you know what will work for you.
After you decide and build, if some of it doesn’t work, you can always change it.
Build with the idea that you may want to make changes, portable stalls and panels are great for that.
Any horse that knows another horse its entire life knows who’s is in charge. They sort that within a couple of weeks, at most. It has nothing to do with liking each other, it has to do with Knowing who to stay away from, who to get out of the way of, and who you can boss around. My mare doesn’t like anyone but she knows how to be in the herd. I have another that hates everyone when it’s feeding time. She still isn’t fed first, because she’s lower than a different mare in the pecking order.
Sure, not every horse can be in a herd and there are certainly specific horses that will never get along, but once they sort the pecking order, there are very few squabbles, and when they happen, they’re mild. (With the exception of something like @Texarkana’s case, which is exceedingly rare)
You are showing your clueless side again.
Very much so.
I am glad your life with horses has been so idyllic that you think this is all true.
Sure, Horse A can know that Horse B is in charge. That does not prevent Horse B from randomly, with no obvious warning, attacking while also closing off the ability for Horse A to leave the space.
Be happy you think this is not how it works sometimes.
Read the great post by @Texarkana above.
To answer your edit to your post after I quoted it - It is not exceedingly rare. I promise you. It is ugly and it happens. Horses can be jerks to each other.
Edit to add - even if we go with what you are saying as fact. The lower level horse never is allowed access to the stall(s). With a more open structure for shelter, the lower horses can get at least part of their body into the shelter if they want to.
Edit to add 2 - If the OP goes the route of open stalls are shelter, they need to have a back up plan for shelter if this goes sideways.
I luckily had the ability to split my dry lot, or Grundy would be long gone.
I wish it wasn’t that way, because now I have to drag another 50 feet of hose out to fill the trough and deal with 2 hay feeders.
Not rare enough for my liking. 
I get where you are coming from. I would have said the exact same thing as you 10 years ago or so. I kept horses like that for years with no issues.
I try not to be the type of person who thinks I need to project my one bad experience onto everyone else. But allowing horses free access to stalls is something that has been debated among horse people for basically ever; there has always been a divide between folks who think it’s okay in the right situation and folks who think it is never okay. I was solidly in the former category for most of my life until I realized why the latter category exists.
I’d put your 4 stalls along the long wall facing the hay barn, add an overhang and runouts opening in to a reconfigured dry lot, move the door on that side to the house side and put the cross ties/wash stall there. Frame up storage/tack room on either side of the cross tie area. Sell the 5th stall or you will eventually fill the need to fill it with a horse. That should leave room to store a bit of hay/implements in the leftover space of the other long wall by the electric panel. Pay the money to trench an autowaterer to the new dry lot. Best money I ever spent (especially in the winter). If you get snow from the direction of the proposed run outs this would be a terrible plan. Good luck. Make the investment it will pay off in hours saved.
Lots of good thoughts and discussion! I should have clarified my stalls as shelters comment - historically the stalls have been their only form of shelter (as in has walls and a roof, there are PLENTY of trees around everywhere). That has meant having to stall them more than I’d like. I wouldn’t ever have a set up with shared access to a stall. My initial proposed layout was to have individual runs out the back of the barn. I’d love to connect the runs to a shared dry lot or have some sort of configuration where someone can feed without haltering and leading them.
I know I said I’d get pictures but I severely underestimated how overgrown everything is. We had horses here up until about a year ago and it has sat vacant since then. First on the list is brush hogging, weed eating, leaf blowing, spraying and then evaluating.
ETA Our one outdoor hydrant also starting leaking so installing that auto waterer outside has gone up the list of priorities since have to dig out the hydrant anyway.
If you do not want shared access to stalls, then I think this is your best bet. You can still feed them as you stated without haltering them and they can be in the runs with access to shelter but freedom to move if the weather is crappy.
Same.
Several of my horses LOVE their sheds, and are in there whenever it’s hot, cold, windy, wet, or Jupiter is aligned with Mars. My mares are fragile princesses, and if they aren’t in their stalls in the barn, they split their turnout time between inside the sheds and grazing.
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