We have identified that when help is called, for example, in qt we don't get any information about that dialog.
It seems that there is not relation set to the dialog, so both can be processed separately. So assuming that pop-up is not set to be topmost dialog.
So solution might be to fix it in the yast module itself and not in libyui.
In ncurses, this part works just fine and we get info of topmost dialog (help in this case)