Nice setup!
Looks like they can get under the coop too?
feathers are mostly protein, and they might be eating the feathers they pick.
stop the scratch and treats. Give them only their feed. If possible get a higher protein feed -either a different layer that is higher protein or an all-flock feed. Layer feed tends to be 16% protein, a minimum required by the birds. So, scratch dilutes their protein intake, so does bread.
put in some visual disruptions if possible and some roosts if possible in the larger run area. A visual disruption will allow the birds to get out of sight of one another, but still escape any bullying. So, a roost helps here or a board propped up against a wall (but not in a corner) where they can enter/leave from both sides.
of nothing else help, “pinless peepers” are said to be very helpful, but I’ve never used them, so don’t have pics or advice on them.