Matthew - you're correct. This type of symbology is lost when importing an *.mxd into an AGP project. I experimented adding the data as a *.lyr file but it returned with single symbol symbology. I then searched for an ArcGIS Idea to add this to the queue of enhancements for AGP and only found one for ArcMap to a feature service but not to AGP. My recommendation is to create an ArcGIS Idea to get this in front of the developers attention. They do see these requests.
