A GeoPackage table can be registered by using the MapBasic Register Table Statement. You can issue this statement from the MapBasic window in MapInfo Pro.
When a GeoPackage table is registered, MapInfo Pro does not write any index or field definition to the associated TAB file. MapInfo Pro does not create indexes on GeoPackage tables by default, because these indexes can get out of synch with the index in the GeoPackage file. This is why the Modify Table Structure dialog box has the Index check box grayed out for GeoPackage tables.
To create indexes for fields within the GeoPackage table, use the Create Index statement. After creating indexes, the field definitions and indexes are written to the TAB file. You can remove the index from the GeoPackage table by using the Drop Index statement.