Hi there,
there isn’t much we can do to adjust the transition of the sticky navigation aside of the settings here:
https://docs.generatepress.com/article/sticky-navigation/
However we recommend that you use enable the Navigation as Header option in Customizer > Layout > Header when using the Sticky nav – its a lot smoother transition.
If you enable that with the Sticky Nav > Fade i may be able to provide some CSS to slow the transition.
NOTE: When using Nav as Header and Sticky nav – its height, which also affects the logo size is defined by the Menu Item height.