In editor you can add an Entity2D or an Entity3D. If you are familiar to ECS, this setup may sound strange, but don't worry there is a reason for that. The Entities don't have type, and this is also true for Godex.

The Entity should just extend Node, and we should not have two versions: however, I would not be able to add the gizmos. To add a new 3D gizmo on the Godot Editor: it's necessary that the node for which this gizmo is created extends the Node3D (or Node2D for 2D).

Modify the editor, so to have just the Entity node, is possible and easy. However, the process to upstream this change require time, so to speed-up the process and support the gizmo ASAP I've decided to follow this route: Have Entity3D and Entity2D.

While this solution is not conceptually correct, it allow to have the gizmo now and since it's not a constraint in any way: it's a great solution. Under the hood, the Entity still don't have a type and you can still add 2D nodes to and Entity3D.