As per a recent discussion (https://community.alteryx.com/t5/Alteryx-Designer-Discussions/Geopackages-Can-Alteryx-Open-GeoPackag...), please add the GeoPackage datatype to the Input tool.
For reference, the open-source project ogr2ogr has this functionality. (https://gdal.org/programs/ogr2ogr.html)
Thanks!