Tom --
Probably the easiest way to do this would be to open the project in the IDE, set the settings in the IDE that you want, and then save.
Even better would be to set up a specific build configuration for these settings, and use that.
The IDE uses MSBuild itself, so any settings that you make in the IDE are saved in the *.DPROJ file (or GROUPPROJ, in your case), and so when you execute the command line, the exact same settings are used as were set in the IDE. If you use a specific build configuration for this specific set of options, you can simply call that configuration on the command line and you'll get what you want.
In other, shorter words: Let the IDE do the work for you.
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