How to send popup windows to background when stopping at a breakpoint?

When developing my r-plugin while being on the road with a single screen, I struggle with Ideas's popup windows not properly going to background when stopping at a breakpoint. This it how it looks:

So basically the popup windows of the debugged Idea instance overlay the development IDE. And it's not just my development Idea window, these popups stay on top of *every* window, there are somehow system-modal (not sure if the term is correct).

Is there any way to make them less "heavy" or to send them to background when stopping at a breakpoint?

I'm running macOS Sierra and the latest v2017.1.

Thanks,
Holger