Always accept the dialog after double-clicking on a file without having to click on the Save button first – irrespective of the single/double click mouse settings. Depending on the application, this will either trigger the dialog's or the app's overwrite warning dialog.
Some history about this:
Accepting the dialog by clicking on a file was removed in: 4ccd77256a0c
Accepting by double-clicking was added in: f729c291cdbb
Accepting by double-clicking was removed again by accident in: 7f08f13809bc