The Meaning of Life, the Universe, and Everything.
The only constructs that require doors are the breeder and the iron golem farm. The trading hall and automated farms should be free of any wooden doors. The breeder only needs to be within the bounds of the village horizontally and outside of the 5-block vertical range in order to work. ImpulseV's design used a 6-door arrangement under the garden, but I see no reason why you couldn't reuse the iron farm's doors for this. You just need to make sure that you have enough doors so that the villagers used to run the iron golem farm are less than 35% of the number of door. Then place the villager breeder and any other uses of villagers, like automated farms and a trading hall at least 5 blocks vertically away, or ship them out to where ever you want.
So my recommendation is to build an iron golem farm like normal, add some extra door so that the population is less than 35%, don't feed them so they never breed and populate the iron golem village too much, build a breeder 5 blocks over or under it, and then build the trading hall and automated farms on the same level as the breeder.