After trial and error I had the geospatial PDF export working using:
arcpy.mapping.ExportToPDF(mxd, Output_File, image_quality="BEST" georef_info=True)
The image quality parameter is important to cut down processing time, and the georef_info does embed the spatial reference, but does not make it a GeoPDF, rather a geospatial PDF that works fine in Avenza or Adobe Reader.
An important note was setting projection of the mxd within the python code before it is exported to pdf. For some reason the WGS84 web mercator doesn't work and that what the data is in on ArcGIS Server. I used a projection for 3005 and applied that to the mxd.
df = arcpy.mapping.ListDataFrames(mxd, 'Webmap')
proj = "//machine/3005.prj"
spatialRef = arcpy.SpatialReference(porj)
df.spatialReference = spatialRef