> You will most likely want to create a default configuration file with sane and sensible default values the first time your program is executed.

Please don't. Include the example configuration in your docs (/usr/share/PROG..) and mention it in the manual. Statistically user will have hundreds of apps installed but will only ever customize a small fraction them. So creating config unconditionally on first run is one of the worst contributors to homedir pollution.

Another argument is version upgrades: if you create configur on first run, you forever bake in the set of options present in that version. If later a new option is added, user will have no idea about it.