@krimar​ I assume you're referring to the Related Table Extension for GeoPackage. No we haven't. FME models the schema but not the data model. For related tables like this - especially with intermediate join tables (mapping table in the OGC spec) - you have to create and keep track of the primary & foreign keys in your FME workflow. Very similar to how we handle this for Geodatabase relationship classes.

This might be a good Idea if you think we could handle this a little more smoothly in FME - perhaps include an example