The rear speakers need to be at ear level if they can be. That is why you will see many setups where the rear speakers are on stands. The placement is something that can be tuned with many receivers, for instance my Sony will let me set the rear to either behind me, by so many feet, where the feet are adjustable, or to the side of me, and I think there are some other choices in the setup. As for the box speaker versus ceiling mount, you can mount the box in the ceiling with only the grill protruding out. I have my rear speakers to the rear of my by one foot, on the ceiling angled toward the listening area, but they are not flush, they are on brackets. You can always get inventive in the palcement, like putting them in a pot mounted tree, fake or otherwise, or put them in the wall to the rear, and put a shelf over them, make them look like they are holding the shelf up. Paint them to match the surrounding area to take attention away from them.
It's always a pain the be a slave to two masters, one tells you to make the sound great no matter what, and the other says to make the sound great as long as I can't see the speakers. I vote for a functional setup, no plastic on the seats, no seats that nobody can sit in.