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Copied over from #160 (comment) below.
Right now we only rename "" to "geometry". Turns out the default GEOMETRY_NAME for GeoPackage is "geom". Not that that is standard though, PostGIS has:
GEOMETRY_NAME: Set name of geometry column in new table. If omitted it defaults to wkb_geometry for > GEOM_TYPE=geometry, or the_geog for GEOM_TYPE=geography.
And MySQL for instance:
The geometry column, which defaults to SHAPE and can be overridden with the GEOMETRY_NAME layer creation option
https://gdal.org/drivers/vector/gpkg.html
https://gdal.org/drivers/vector/pg.html
https://gdal.org/drivers/vector/mysql.html
It should be turned into documentation per #160 (comment).