I don’t know what your facilities look like, inside or outside. How big is the coop, how big is the run, or are they allowed to free range on grass. How hard would it be for chicks to get through the pop door? It’s hard for me to make specific recommendations when I don’t know what I’m working with. There is no right way that everyone needs to follow, just a lot of different ways we do this, but your facilities and set-up may make one way better than another.
I have an 8’ x 12’ coop, a 12’ x 32’ main run, and a large grassy area inside electric netting. My pop door is about a foot above the coop floor so I stack pavers inside and outside to make steps to help the chicks get in and out. I handle my broody hens and chicks two different ways.
If my coop isn’t very crowded I let the hen bring the chicks off the nest when she wants to. I put food and water where the chicks can get to them on the coop floor. That’s it, I leave everything else up to Mama. Usually she keeps the chicks in the coop for a couple of days after bringing them off the nest. Then she takes the outside. After that they pretty much spend all day every day outside from morning until night. She brings them back into the coop at night to sleep, usually in a corner on the floor.
If my coop is fairly crowded I wait until Mama brings the chicks off the nest and then lock them in a shelter I have inside that electric netting. I leave them in there for about three days and nights, then open the door. After that the hen keeps them outside all day and takes them back to that shelter at night where I can lock them up.
I always have at least a rooster and other adult hens in the flock. Often I have other juveniles. I have never lost a chick to another adult in the flock. One time I had several 8-week-olds in a grow-out pen. A 2-week-old chick got through the gate into that pen and away from Mama’s protection. She could not get in there to protect her baby. The 8-week-olds killed it. I quickly fixed that gate. As you have seen it’s pretty easy for them to slip through things. To me that’s the biggest risk of trying to keep them separated, the chicks may get to where Mama can’t protect them.
Some people separate a broody hen during incubation, during hatch, and/or while she is raising her chicks. They have their own reasons for that. I’m not trying to say they are wrong, it’s just not the way I do it. But I have lots of room, not everyone does.