I know this is a lousy constructed answer, but I've just been playing with the UIPopoverController's views. They do exist.
The only way to access them is from your view that is sitting in the UIPopovercontroller.
I have a navigation controller so I follow this hierarchy
UIView *test = ((UIView *)[[[self.navigationController.view.superview.superview.subviews objectAtIndex:0] subviews] objectAtIndex:1]);
UIView *test2 = ((UIView *)[[[self.navigationController.view.superview.superview.subviews objectAtIndex:0] subviews] objectAtIndex:1]);
test.backgroundColor = [UIColor greenColor];
test2.backgroundColor = [UIColor greenColor];
This isn't exactly the end goal, but it is really close.
you'll find that the_view_in_the_popover.superview.superview
(maybe just one superview if you are not reaching out from a navigation controller view) is a UIPopoverView. If you cast it as a UIView and treat it as a UIView you're not really breaking any rules. I guess that is really up to apple though.