Regardless of what you use, this is about when you have that capability and you have XY on top, the confirmations come out NOT ON TOP. AOT is a misnomer since what's on TOP is always relative with more than one window AOT.)
So what you do, when you know this is happening, and you get a ding when you try to do anything else because the active window can't be seen and is monopolizing pending confirmation? - You use the window menu shortcut key ALT-SPACE and select ALWAYS ON TOP. The confirmation window will then appear. You can't do anything else in the circumstance except move the confirmation window somewhere else the same way - or turn off AOT for the main (in this case XY) window.
But for standard confirmations ("Move ten items to recycle?") you want/need those to always be AOT because they don't have to be answered and the process just sits there. You will eventually wind up with unknown consequences as operations continue in parallel, and you accumulate numbers of the same exact message. WORSE, basic message windows don't have a WINDOW MENU to manipulate - and you have to put the peanut butter on the cheese with the mouse.
XYplorer Beta Club