If we don't do that, the default options get mixed up with theme modules (including our own theme_bootswatch).
Even worse, when installing any theme (including theme_bootswatch), the menu to change these options is replaced by the new theme one, so you cannot disable the broken options.
This trick allows theme modules to disable the default options so they don't conflict, while restoring the user choices when uninstalling the theme.
David Monjoie
5a6d2f6e23