[fortysixdegrees]

I feel you should retract this comment so as to not mislead people. See extensive spatialite documentation on spatial operators here: http://www.gaia-gis.it/gaia-sins/spatialite-sql-4.2.0.html

[dvisca]

But GeoPackage, which the question referred to, does not support spatial functions in and of itself. But I also wrote that you can use e.g. SpatiaLite to apply spatial functions to geometries stored in GeoPackage. But then this is not really different from using any other application like QGIS or gdal.