The Navigation logo size is defined by the height of the Menu items set in Customizer > Layout > Primary Navigation –> Menu item height. Let me know if that works, i can’t access the link – can you check the URL
In Customizer > Layout > Container – change the Content Layout to One Container.
The alternative to using the Navigation as the Header is to use the normal Header with your Logo and set the Primary Navigation to float right. This will provide more control over the logo and the nav.