In Directory Opus 13.10 we added ways to make Preferences and Customize open differently. I forgot we had just added this, but just remembered.
For Preferences, you can edit the menu item to make it open over the window that opened it:
Prefs POS=lister
Or over the mouse pointer:
Prefs POS=mouse
Similarly, for Customize:
Prefs CUSTOMIZE POS=lister
Prefs CUSTOMIZE POS=mouse