You'll be able to have an area with any content you like sitting above Flarum's header bar. Once the page is scrolled down past that content, Flarum's header will stick to the top. Kind of like this.
So you'll be able to put your big logo in that pre-Flarum content area, and then a smaller one in Flarum's header.
If you're really game, you'll be able to apply your own styles to Flarum's header to make it taller/shorter/whatever, but that won't be recommended.