When in the game list for a certain system, if you hit Select on a ROM, then edit metadata (or something to that effect), after the list of all the info the system has on a game (game name, ROM name, date, star rating, etc.) on the very bottom is "delete". Still super-time intensive if you have complete romsets of like 3,000+ games for a certain system, but the option is there at least.
For backing up configs, if you're ever made a USB stick with a "retropie" folder on it and inserted it into the Pi it'll make a "to" and "from" config folder for you - I've honestly always wondered how this works and exactly what it backs up, and if you edit a file on your PC, then insert it into the Pi if it automatically look at the dates of the two identical files then overwrite the older version of the two or what...