Sadly it's never quite as simple as that. Assuming it could be made to work, there is also the reality of maintaining and testing the integration point with all source control systems that are integrated with Visual Studio. With the rate of change in this area, such investment would take time away from adding critical features to make NCrunch work better for a much wider range of users.
Something that may work for you would be to edit the NCrunch project configuration files directly as XML resources that are included in your projects. This way VS would automatically check the file out if you were to change it. The XML format isn't complex and NCrunch should automatically pick up any changes after you save them to disk and reset the engine. NCrunch will only save data to the project configuration files directly after you make changes in the configuration pane, so provided you commit to writing the configuration yourself, you shouldn't have problems with your changes being overwritten.
I hope this helps!
Cheers,
Remco