Hi there,
Thanks for the heads up here. We have a full rebuild of our Typography structure planned for GP 3.1.0 and GPP 1.13.0 which will address issues like this.
For right now, there is a “hack” you can apply. You can overwrite the System Stack value to the value you need:
add_filter( 'generate_typography_system_stack', function() {
return '"Palatino", Palatino Linotype, serif';
} );
Then choose “System Stack” in the Customizer.
Less than ideal, but it will work until we release the new typography system 🙂