Not sure I buy this. If you have a config header file and make backwards incompatible changes to it how is that different to having backwards incompatible changes to any other config system?
I think what the author meant to say is "don't make breaking changes to your config system". Maybe it's common to ignore that when using source code as config; I don't know.
It's a bad idea anyway because compile-time options should generally only be for configuring the presence of optional third party dependencies, which you can do automatically. Anything else should be a runtime option.
As a gamer, I couldn't agree more. Put all the video and audio settings in the options menu; especially if they are things easily changed by editing an .ini file in the install directory. I'm also big on having modding tools like the Creation Kit for modifying the game without having to edit code or use command line conversion tools. It's just a massive time-saver.