You can always divide your run into 2 sections. A more secure part that is roofed and hardware cloth that they can access 24/7, and a bigger area like you described for daytime..
This is a great suggestion! I have my run split though I rarely close the door between the halves. But back when I was having hawk issues I was able to net off one side while we worked on securing the other (two different fence heights, so just throwing netting on the whole thing wasn't going to work).
Split runs also makes it easy to do maintenance on the run, since you can lock the flock on one side while working on the other.