I see no pictures yet.
You asked "why is it bad for chickens to sleep in the nesting boxes?"
People are trying to tell you and you keep responding with your reasons why you should allow them to continue to sleep in their nesting boxes/ sleep boxes whatever you want to call them.
So, are you asking a question or do you just want to argue?
People are trying to explain to you.
When chickens sleep, they poop A LOT.
1. If your chicken is on a roost or perch, when they poop, the poop falls away from their body. RIGHT?
2. If a chicken sleeps squatted/sitting/lying down, they poop underneath themselves during their sleep time. Right?
3. Therefore, they are literally sitting in/on their own poop the entire time they are in the boxes. RIGHT?
4. Therefore, we DO NOT think it is a sanitary or a healthy idea to allow your chickens to sleep ontop of their own poop.
5. It doesn't matter if they scratch up the poop in the morning, it doesn't matter they don’t lay eggs in those boxes.
6. What matters and is unhealthy for your chickens is to sleep/sit or rest on their own crap. Period.
7. That behavior has many long term consequences.
8. Look at it this way:
Do you think sleeping in your own poop and pee all night long is unhealthy or bad?
9. If so, why do you allow your chickens to do it?
10. That's all that people are trying to tell you.
11. Good Luck with whatever you decide to do, after all, they are Your chickens.