It seems you've removed the default.cfg execution.
This was a mistake. There is no longer a way of providing a default configuration with e.g. nQuake without having a config.cfg. Once a user changes a variable, there is no other way of returning to the default configuration other than re-downloading nQuake. If you would've kept default.cfg as it were, the user would've simply had to type cfg_reset and boom, default configuration. Perfection at an arm's reach.
Also, there is the problem of video settings getting applied before autoexec.cfg gets executed. Bringing back default.cfg would allow one to provide default video configuration without having a config.cfg bloating the directory or forcing video settings on the user by using command line parameters.
Please bring default.cfg back, now.