she will probably bring them out with her during the day1) If we open the crate during the day after the chicks hatch is there any danger of them wandering into the run on their own or will she keep the chicks inside the crate with her?
that won't arise if you open the crate door. As you've explained it, the crate is only for protection against night time visitors. So I would have the crate door open all day every day before and after hatch. Treat the crate door like the pop door to the coop. Keep the food, drink, dust bath etc. outside the crate.2) Is having her in the confined space of the crate setting her up for confrontations with other flock members who might go inside to check out the new chicks?
Other flock members will be curious and will want to meet the new flock members. They will hear the chicks cheeping before you do and may even hang about nearby waiting for a glimpse. But in my experience they will not harm the chicks. And if the broody thinks one might, she will deal with it more appropriately than you or I ever could.
I would urge you to try not to interfere. She instinctively knows what she's doing. Just sit back and enjoy from a distance.Is there anything else I should be taking into consideration?