I suppose you could present it as either drop the floor or raise the openings and let him decide what seems more workable?
Here's some food for thought in re: chickens in the rafters up by the ventilation:
The Queens Have Conceded ...
10F in Central North Carolina in an Open Air Coop
I...
Yes, you have a legitimate concern there.
Using Deep Bedding in a Small Coop
I'm afraid that I don't have any ideas on how to fix the problem with the framing and floor completed. :(