2008 sln is really dumb, they only have lists of projects / files that can be placed in the solution explorer and project dependencies, so I don't think this is an option.
My gut instinct must do something with relative paths. For example, in your stdafx.h you can # include ".... \ project_configuration.h", then to build sln a you will check things in one directory and sln b another. Each of them will have a separate project_configuration.h.
I believe that you could do something similar with vsprops files, which are essentially #includes for vcproj files, although I found them a little annoying to maintain over time.
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