The Navigation Menus panel is for Mai Theme settings specific to the available menus and menu locations. If you aren’t using a menu location, the alignment settings will not be available until you set a menu to use that location.
These settings can be accessed via Customizer > Theme Settings > Menus.
Navigation Menus > After Header
If you have a menu location set to After Header, you can set the alignment to Left, Center, Right.
Mobile Menu Breakpoint
The largest screen width at which the mobile menu becomes active, in pixels.
Menu Alignment Settings
These self-explanatory settings allow you to align each menu location in a specific position.