This would be cool but since the template is strictly designed around 2D sprites, adding full 3D model support would require significant changes to the core logic and resource framework.
Because of this, it won't be covered in the official guide. However, if you're comfortable editing GDScript, you could theoretically attach a 3D mesh node to the enemy/weapon scene and hide the main sprite node as a workaround.
If I ever get a chance, I might drop a guide for it.