Well... Perhaps excellent, but not entirely correct. I suppose I should point out that it I was being brief so the post was not 100% accurate. So much for saving some time by doing less explaining and typing...
It also happens to people who play at the default resolution, but they would be less likely to notice. It still resets the options other than the resolution to the default values, like whether or not automated workers chop forest and the various sound settings as well as the graphics quality settings. If someone never changed a single option on the option screen, then it might be inconsequential except that I seem to recall the it resets the audio to be mono rather than the more likely to be correct stereo.
The only way to stop it from happening without the workaround and without using the SVN version (until the next version is released) is to never play any Civ4 without C2C and only launch it from a shortcut set up to load the mod so that regular BtS is not loaded before C2C (you can't avoid the issue if you run BtS and select C2C via Load A Mod in the menu). It's the switch between non-C2C and C2C (in either direction) that results in the problem. The workaround changes the loading of the mod so C2C uses a different profile just for it instead of resetting the default profile to a version that is incompatible with regular BtS and most (if not all) other mods. But most of that was covered in the post in the link.