For printer option settings (in a printer entry click the gear button, then "Printer Options" in the pop-up menu) CUPS support system-wide default and user defaults. To change system-wide defaults CUPS modifies the PPD file of the queue in /etc/cups/ppd/ and user defaults are saved in ~/.cups/lpoptions. User defaults override system defaults.

The option settings dialog shows the settings which are valid, for options not modified by the ~/.cups/lpoptions file it shows the system settings from the PPD. So this is correct.

The problem is what happens if one modifies the options and clicks "Close". One does not know what gets changed and if something gets changed. For a normal user (not in "lpadmin" group) changes should be saved in ~/.cups/lpoptions, for a user in the "lpadmin" group there should be a button to save as personal defaults (in ~/.cups/lpoptions) or system-wide (in PPD file).

In any case there should be a button to reset to system defaults (removing changes in ~/.cups/lpoptions).

All changes should be done using appropriate CUPS API calls if possible.

My observation is that changes seems to be done always in the PPD file (working as a user in the "lpadmin" group) and the presence of a ~/.cups/lpoptions file is totally ignored, letting changes on options present in ~/.cups/lpoptions looking like they are ignored, as the setting of ~/.cups/lpoptions is always displayed and so the change in the PPD file does not get visible. This leads to total confusion.