I've never tried specifying multiple .dty files with the MS_GEOCOORDINATE_USERLIBRARIES variable, but since the variable name is plural it seems logical that you should be able to. In that case you wouldn't have to switch libraries between projects. If that works and you still want to merge them you can activate Bentley Map from within PowerInRoads or PowerGEOPAK and copy the custom GCS from one .dty file and paste them in to the other.
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