Every QGIS project file can have multiple print compositions which are listed in Composer Manager. These compositions are stored within the QGIS project and don't have to be saved separately. And QGIS projects can be saved in a GeoPackage.
Additionally, a QGIS-user can create print templates which can be reused in different projects. They can be saved/loaded from within Print Composer and can be stored in any folder.
But I'd like to know whether it is possible or not to store .qpt files in a GeoPackage WITHOUT saving print compositions in a QGIS project which is stored in the GeoPackage?