FBX or Blend?

Is there a difference between the .blend and .fbx models?

Not really aside from space required on disk.
Mind you however that .blend is a blender extensions, and as such it can be opened in blender only and would probably require external plugins on different applications, while FBX is a more “universal” (it’s actually a proprietary file owned by Autodesk), and you can open it with pretty much whatever you want.

From what I understand, when you import a .blend file in to Unity, Unity actually invokes Blender’s fbx export module to export the .blend file to an .fbx behind-the-scenes.

Yes, there’s a difference between .blend and .fbx models. A .blend file is the native format used by blender, which keeps all your scene data like materials, lighting, animations, and modifiers exactly as created. On the other hand, .fbx is a more universal format mainly used for exporting 3d models to other platforms or software like unity, unreal, or 3ds max. When you export from blender to fbx, some data like complex shaders or modifiers might not transfer perfectly, so it’s mainly used for sharing or importing into other tools rather than editing inside blender. Source merino protect.