Ideas
I'm playing with chickens in my current save and I noticed the same thing. Chickens never incubate the eggs, roosters don't show up on the blacony. The only animation that is working correctly is going into the coop, cause the animation of getting out of the coop is also broken. Chickens spawn underneeth it and walk though it instead of using the stairs.
Just recheck your comment and realize that you talked about another visual bug...
the animation of getting out of the coop is also broken. Chickens spawn underneeth it and walk though it instead of using the stairs.
I haven't noticed this because there are many missing animations in this game. But right, when I summon them, they pop up on the ground like your post. Animation of going to the coop is still fine.
The bug in this thread may not be as critical as others, but I hope that when this bug is fixed and also resolve this issue.