A DESCRIPTION OF THE PROBLEM :
javafx.scene.control.dialogs report that their _NET_WM_WINDOW_TYPE is "NORMAL" instead of the more appropriate, dedicated "DIALOG".

Some window managers use this property to handle the window. Typically, tiling window managers will tile "NORMAL" windows which is not desirable for Dialogs.

It would be better if JavaFX Dialogs reported the proper window type.

https://specifications.freedesktop.org/wm-spec/latest/ar01s05.html