This is just a specific case of "what if the program I'm using doesn't have a config file option for X" though. I usually run into it with webserver config fil

This is just a specific case of "what if the program I'm using doesn't have a config file option for X" though. I usually run into it with webserver config files where (in both apache and nginx) I have to do something moderately contorted to get the end result I had in mind, but in the end the general case is just another trade-off.