R – Web Deployment Project with an replacement .config geting “changed”

It seems like your build setup is not generating the private accessor assembly. As a result, you're getting that missing using directive or assembly reference error. You can look at Publicize tool to generate the private accessor during your build process. It is mentioned in there that

The generated assembly is also known as a private accessor. You can also generate private accessors from the IDE, but you might use publicize.exe instead in Automation, scripting, and build scenarios.

I use private accessors as well in some of the tests and use TFS TeamBuild and MSTest. Private accessor gets generated during builds. I did not have to do anything manually.

I used CruiseControl with NAnt extensively, but not MSBuild. Do you have different MSBuild files for each build type (i.e. local/test/prod)? Could you have a single one that can be parameterized such that your CCNet integrators can explicitly call the appropriate options for the target environment? That's how I have my continuous integration versus release candidate builds configured in CCNet. A single master NAnt build script and a different CC integrator for each target env with the necessary build parameters (be them targets or property values). I imagine you could do something quite similar with MSBuild vars/targets.