If you call the scan popup with the hotkeys the expected behavior is to bring the scan popup window to the front and get focus to be able to browse the result and optionally input a new search. As GD is cross-platform this behavior has to be tested and be consistent in a great number of setup (not only the tipical Windows and OS X versions but considering the different options of Window Managers present in Linux/X11). Here you can see a table with some tests I carried out in the past
https://github.com/goldendict/goldendict/issues/194 At that time they were several issues with the bring to front expected behavior. I think we will have to carry another test session because some of those issues were resolved.
What I understand you are suggesting is to have an option in GD to NOT allow the popup window to appear in front of all applications. Although I understand the motivation for such an option and it seems simple to add it's not for the reasons explained before. I would suggest you other alternatives:
1) Setup GD to trigger scan popup with a combination of modifier keys such as Ctrl + Shift. Or disable such function and just select the word you want to translate and press Ctrl + C + C.
2) Pin the scan popup window change the window dimensions, unpin the window again and next time it appears in front of your other applications you just can hide it by quickly moving the mouse cursor over the window and out of it.
There is an interesting feature request that could ease somehow your issue
https://github.com/goldendict/goldendict/issues/81Hope it gets implemented in GD some day soon.