Hi there,
this is the latest doc for Navigation as Header:
https://docs.generatepress.com/article/navigation-as-a-header/
If that option is enabled it will use the Logo you set in Customizer > Site Identity.
From within the Customizer ( ie. Global changes ) you can add a different logo for Mobile Header and for Sticky Navigation.
The logo options in the header element ( as per the doc you linked to ) should only be used if you need to dynamically change what logo is used. Such as a different color logo on pages that have a merged header.