Hi there,
That’s because the navigation as a header option is activated:
https://docs.generatepress.com/article/navigation-as-a-header/
So the logo size is determined by the menu item height:
https://docs.generatepress.com/article/menu-item-height-width/#height
The main issue in your case is that there is a large amount of top and bottom padding in the logo image.
https://www.screencast.com/t/YC4vYaAji65
You would want to recrop the actual image so there are only minimal paddings all around the logo.
You also don’t need to make the logo 4500px big. Something around 200 should do.
Let me know if this helps 🙂