Square footage recommended minimums aren't supposed to include the space taken up by nest boxes, feeders or waterers. It's only space that's available to the chickens. They also are recommendations of minimum spacing, not the optimum spacing that the chickens would do best at. That being said, they are only recommendations.
One aspect of spacing is behavioral, in that over-crowding can cause aggressive pecking problems. The breeds you keep and your climate combined with your run size/style, can really vary your outcomes.
The other aspect of spacing is pretty simple. Poop!
The more crowded a coop is, the bigger the poopy mess is and the more time you have to spend cleaning it. How often do you want to clean your coop? Daily, weekly or yearly? I would never want to have to clean my coop every single day of my life, just to have a few more chickens. To someone else, it's totally worth it.
At 5 sq. ft. per chicken, a coop is pretty effortless. Occasionally sprinkle a little fresh litter on top and scoop out the old litter once a year. At 3-4 sq. ft., you're going to have varying degrees of crusty poop on the surface of the litter that you will have to either break up and stir in or remove, every few days. Less space than that and you are getting into the territory of daily scooping, or dropping pits that further reduce available space or dropping boards that you have to regularly scrape stuck on poop off of.
All of these systems work. It just depends on your own likes and dislikes, which way you want to go.
Edited to add that I was talking about full size chickens, not bantams. And I can't believe my spell checker doesn't think poopy is a word. Have they never lived with chickens, a puppy or a baby???
