In the FME top ribbon, click the Add Reader button
A dialog box will appear.
The Coordinate System should also be set appropriately.
Click Parameters in the Add Reader dialog box
Another dialog box will appear to specify OGC GeoPackage Parameters.
FME OGC GeoPackage Parameters dialog. Here, specific layers within the GeoPackage can be selected, rather than importing the entire file. Additionally, the Search Envelope can be used to clip the GeoPackage to an extent.
Select the layers to be added into the workbench
FME GeoPackage Select Tables dialog. Click OK when the required themes / layers have been selected.