Sorry, Nabble did not include my ogr2ogr command to the mailing list mail, reposting.
You can do the join as suggested in http://www.geopackage.org/modeling_guidelines.html by converting the first geometry with all the attributes into GeoPackage as you have done, and then adding another layer with a command like ogr2ogr -append -update -f gpkg -sql "SELECT second_geometry AS geometry, id AS id from table_with_two_geometries" my_geopackage.gpkg -nln table_with_second_geometry_to_be_joined PG:..... -Jukka Rahkonen-
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