### 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)

base = area;
							} break;
						}
						for (const Ref<Shape3D> &E : shapes) {
							CollisionShape3D *cshape = memnew(CollisionShape3D);
							cshape->set_shape(E);
							base->add_child(cshape, true);
							cshape->set_owner(base->get_owner());
						}
					}
				}
			}
		}
	}
	
	if (Object::cast_to<ImporterMeshInstance3D>(p_node)) {
		ImporterMeshInstance3D *mi = Object::cast_to<ImporterMeshInstance3D>(p_node);
		Ref<ImporterMesh> m = mi->get_mesh();
		if (m.is_valid()) {
			if (node_settings.has("generate/navmesh")) {
				int navmesh_mode = node_settings["generate/navmesh"];
				if (navmesh_mode != NAVMESH_DISABLED) {
					NavigationRegion3D *nmi = memnew(NavigationRegion3D);
					Ref<NavigationMesh> nmesh = m->create_navigation_mesh();
					nmi->set_navigation_mesh(nmesh);
					if (navmesh_mode == NAVMESH_NAVMESH_ONLY) {
						nmi->set_transform(mi->get_transform());
						p_node->replace_by(nmi);
						memdelete(p_node);
						p_node = nmi;