1. Correct: Ticking them will allow managed apps to see unmanaged data and vice versa. Obviously this is downgrading the security of the device a little, so have a think about the consequences of doing so.
2. Tags are the answer. As the screenshot below, I've gone to profile configuration, and, because I want to EXCLUDE devices from this, I've selected WITHOUT ANY of the following tags and created a tag called ExemptFromStuff. I've then tagged the device with the same tag. This should exclude the device from this policy. Obviously, there's a tonne of flexibility here