### Godot version

4.0 beta 15

### System information

Windows 10

### Issue description

When ticking `apply_root_scale` the scale is not applied to custom collision shape set in importer.
This apply for `shape_type`  Box, Sphere, Cylinder and Capsule

_I tried to fix it myself but i'm a bit confused on how to have acces to the `apply_root_scale` and `root_scale` at the moment where the shape is generated_

### Steps to reproduce

- Add a 3d model.
- Generate physics for the mesh
- Select a `shape_type` for example Box
- Add `root_scale` != 1 and tick `apply_root_scale`

### Minimal reproduction project

[BoxColliderImport.zip](https://github.com/godotengine/godot/files/10500751/BoxColliderImport.zip)

const BodyType body_type = (BodyType)node_settings["physics/body_type"].operator int();
						switch (body_type) {
							case BODY_TYPE_STATIC:
								mesh_physics_mode = MeshPhysicsMode::MESH_PHYSICS_MESH_AND_STATIC_COLLIDER;
								break;
							case BODY_TYPE_DYNAMIC:
								mesh_physics_mode = MeshPhysicsMode::MESH_PHYSICS_RIGID_BODY_AND_MESH;
								break;
							case BODY_TYPE_AREA:
								mesh_physics_mode = MeshPhysicsMode::MESH_PHYSICS_AREA_ONLY;
								break;
						}
					}
				}
				if (mesh_physics_mode != MeshPhysicsMode::MESH_PHYSICS_DISABLED) {
					Vector<Ref<Shape3D>> shapes;
					if (collision_map.has(m)) {
						shapes = collision_map[m];
					} else {
						shapes = get_collision_shapes(
								m->get_mesh(),
								node_settings);
					}
					if (shapes.size()) {
						CollisionObject3D *base = nullptr;
						switch (mesh_physics_mode) {
							case MESH_PHYSICS_MESH_AND_STATIC_COLLIDER: {
								StaticBody3D *col = memnew(StaticBody3D);
								p_node->add_child(col, true);
								col->set_owner(p_node->get_owner());