Your coop may not be as bio diversible as outside in the poo palace, so stuff building up in there may do worse things to them than a pile under a non native tree. I don't think anybody really wants to do that kind of work, microscopic or otherwise but I am pretty sure most DO want to keep their birds healthy. People used to live in caves. Maybe you should get rid of that toilet, that IS overkill, and a huge waste of water, why don't you just poop into a pot and when it gets full, throw it out the window, you know, like they used to do?
I don't want to be sleeping with no stinky dogs in my bed either FWIW, warm or not. I HAVE seen chickens though that DO like the petting thing. The tractor supply out here, one guy comes in and brings a silkie he puts in the darned shopping cart, with a little perch thing he made up and goes around the store with her. She gets all kinds of awws and ooh she's so cute and pets and scratches and loves the attention it seems. Chickens like dogs I would believe probably have different personalities, and some do like to be pet, just like some of those quivering urine dribbling little mutts that the hollywierd types like to carry around in their purses like to bite anything that moves and don't like to be pet. Some do, some don't.