It is impractical to build and export everything as one piece. I mean, theoretically you could export the whole scene as a gltf with animations blend shapes and all, but then managing those assets might become a pain. You could import your Blender scene as your main scene, save it as a native Godot scene and add extra assets there. However, I have noticed some issues with saving some properties in such scenes, some of them seem troublesome to save and manage.
I would advise you to adopt a more modular approach and save your basic layout from Blender as a gltf and the rest of your trees and assets as separate gltfs. That way you have easier control over them from your main scene.