Sure, but Geopackage is a transport format: it describes itself as "a format for transferring geospatial information". Spatialite is a spatial analysis databas

Sure, but Geopackage is a transport format: it describes itself as "a format for transferring geospatial information". Spatialite is a spatial analysis database: it describes itself as "a complete and powerful Spatial DBMS (mostly OGC-SFS compliant". They both use the same container, SQLite. And indeed there are other geospatial formats built on SQLite, such as mbtiles. But the intents are very different.