The WPF popup should behave like it's parent app:

If it's parent app is behind another window, the popup should be also.
If you switch to another app, you should be able to click on controls in the popup - not have to click on the parent app behind it first.

If the official word is "use tooltips or child windows always instead of a popup" then they should be depreciated. I believe right now they are a trap for inexperienced developers because the limitations are so unexpected, leading to a lot of wasted time trying to fix.