Update on this: I believe the has_custom_header() || has_custom_logo() PHP code doesn’t fire, which is below the #nav-bar in the themes header.php file.
I manually added the <?php the_custom_logo(); ?> code further up the page where Site Title is, and the logo displayed and was adjustable in the Customization menu with size, position etc.
Anyway, they are my observations on the matter.
It’s likely I have something setup wrong which is stopping custom headers being used or something. So if you check my link, you’ll see a logo, but its because I coded it to be there, you’ll see that from source code.