As far as I understand it, you would have to modify the color scheme file to support what you want. Bundling the colors as part of the tmLanguage file doesn't make sense anyways. By doing that, you would basically be saying every user has to use your predefined colors, which I could imagine people wouldn't like. For example, let's say I have a white background, and you decide to make the text color white. It would look like there is nothing there.
I think the best route is to include sample "extension" of the color scheme file. Then allow the users to modify it themselves as they see fit. This would also let you use the standard naming conventions, so if they don't apply any new scopes, everything still looks okay. Of course, they can specify a more detailed scope in the scheme file to apply the proper text color/background.
What I think would be nice was if there was some way to simply extend a color scheme from a separate file, rather than needing to modify the original. Though that doesn't exist.