The coop has nest boxes. They will have free access to the coop and the run during the day. We do not get a lot of rain in SoCal but when it does rain it rains heavy. I am sure I have not thought of everything but I am learning.
I have a side alcove like your photo that I had to fence off from chicken access. We had Leghorns that were smarties and almost escaped that way. I saw them eyeing the fence ledge and the jump up so we double fenced off the alcove so they couldn't figure out an escape. Watching our chickens gives us our needs for adjustments.