Previously, the customize window was always on top, but now this is not. When you try to drag icons onto it, it hides.
It's no longer on-top to make things easier on single-screen machines. Instead, buttons appear in the main window's titlebar to bring it back to the front or click OK or Cancel in it without having to find the window at all.
Dragging buttons to it can be used to delete them, if it's side-by-side with the window you're editing, but you can also do that via the right-click menu (e.g. if the main window is maximized and the Customize window is under it).
Btw I prefer it very much like that than the way it was before. When you want to rearrange buttons on toolbars, look for the code of another button on another toolbar (I have severals dispatched on top & bottom of listers), the customize dialog was ALWAYS getting in the way (Murphy's Law ???) !
So customize window behind and the clever OK/Cancel buttons on top of lister are a great UX improvement for me.