Megalomaniak
To clarify this is when loading a project after starting the Godot Editor.
My main scene is a splash screen with a couple Controls, TextureRects, and a Node as a root.
But your comment made me re-think this. I changed the root to a Control and now it opens as a 2D scene. I think by having Node as a root, it wasn't sure what to do, so it went with 3D