One reason you get such a variety of advice is that a lot of different things can work. A really huge reason different things can work is that we are all unique. We keep chickens in such different conditions and climates, with different flock make-ups, using different management techniques, and having such different goals that no one magic number works for us all. You might follow the link in my signature to get my opinion of what some of the different considerations are but I don’t give magic numbers.
While you need a minimum amount of space in the coop so you can put in roosts, waterers, feeders, and nests so they don’t poop in things they should not while on the roosts and give them a clear landing spot when they hop down from the roosts, the amount of square foot per bird in the coop is not what is important. What is important is how much space they have available when they need it. That space could be in the coop by itself, in the combined coop and run, or they could sleep in trees and have no fence at all. If you leave them locked in the coop by itself when they are awake they need a fair amount of room in there. If they have access to more outside space when they are awake the coop size isn’t that important.
Will one rooster be too much for one or two hens? Maybe, maybe not. Many breeders keep one rooster isolated with one or two hens throughout the breeding season and do not have any over-mated, over-stressed, bareback hens. One of their secrets is that they use mature chickens, both male and female. A lot of people like to blame the rooster for everything but the hen has a part to play too.
You can still have problems even with consenting adults. Some hens have brittle feathers that break off and leave bare spots even if the rooster is doing nothing wrong. Some males are brutes that never develop good technique. Some hens won’t accept any rooster and resist, which can lead to conflicts and forcing.
The vast majority people that have with chicken mating problems are talking about juveniles, not adults. Pullets and cockerels mature at different rates, even individual pullets and cockerels mature at different rates. The cockerels especially can have their hormones running wild, can’t control them, and have not developed good technique. The pullets normally mature slower and don’t have a clue what is going on so they don’t cooperate. Watching a flock of immature cockerels and pullets maturing into consenting adults is not for the faint of heart. You may find that disturbing, especially if they are in closed in spaces. There is some risk involved too, especially if the pullets don’t have enough room to run away.
That’s where the magic numbers for space really break down. It’s not how many square feet per chicken do you need. It’s do they have enough room to interact socially with based on age, sex, and the individual personalities of the chickens. That is going to be unique for each of us.
With your room the way I understand it, if they have access to the runs when they are awake, you will probably have enough room. But you may need to water and feed and have nests in the run in the run for that smaller coop. I just don’t see how you can lay out a 2’x4’ area as anything other than just a safe place for three chickens to roost.
If it were me, I’d take down that partition (after trying to integrate them all to see how it goes) and let them all run together. I don’t know what your objections to fertile eggs are, but if you don’t incubate them they won’t develop or hatch. Good luck but I think you are trying to make it a lot harder than it has to be.
