Most Debian packages I can think of ask something like: "existing config found: use, overwrite, manually merge?"

dispatch-conf is a more advanced version of this.

Or just, properly handle pre-filled configs instead of being lazy?

Some programs I have used will set up a 'new install' mode where the program will find no config file exists, and so will ask the user what options she would like to use, and creates a new personalised config file accordingly.

If I remember correctly, a few decades ago the mail program 'elm' did this.