Hello pyeah,
addGeoid() should be used only to add the geoid to the list, if it was not automatically added to the list of available geoids when the application started (i.e. was not in the /geoids/ subdirectory of PhotoScan Pro installation folder when the script was started). It wouldn't modify the coordinate definition.
To initialize WGS84+EGM96 height coordinate system I can suggest to use WKT definition (as the system doesn't have the EPSG registry code):
chunk.crs = PhotoScan.CoordinateSystem('COMPD_CS["WGS 84 + EGM96 height",GEOGCS["WGS 84",DATUM["World Geodetic System 1984",SPHEROID["WGS 84",6378137,298.257223563,AUTHORITY["EPSG","7030"]],TOWGS84[0,0,0,0,0,0,0],AUTHORITY["EPSG","6326"]],PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],UNIT["degree",0.01745329251994328,AUTHORITY["EPSG","9102"]],AUTHORITY["EPSG","4326"]],VERT_CS["EGM96 height",VERT_DATUM["EGM96 geoid",2005,AUTHORITY["EPSG","5171"]],UNIT["metre",1,AUTHORITY["EPSG","9001"]],AUTHORITY["EPSG","5773"]]]')