I've been wondering about this part because we're having a fairly heavy rain with some intermittent lightning and thunder today. I was thinking we might just go through some scratch into the coop and keep them in there until the storm passes. Are there no sanitary issues here if they are stepping around in their poop / scratching for food in it?
One of the things with the deep bedding is that because you have so much of it the poop will quickly dry out and become harmless.
I've never managed to convince my birds to stay out of the rain completely. They go in and out and sometimes look half-drowned, but they're always OK.
This thread might be reassuring: https://www.backyardchickens.com/threads/wet-hens.1442537/
I've even seen my birds out foraging in their run between rain bands during tropical storms.