### 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)

CRASH_COND_MSG(descendants.is_empty(), "This is unreachable, since the collider view is always created even when the collision is not used! If this is triggered there is a bug on the function `_fill_scene`.");
		MeshInstance3D *collider_view = static_cast<MeshInstance3D *>(descendants[0].operator Object *());
		collider_view->set_visible(generate_collider);
		if (generate_collider) {
			
			
			Vector<Ref<Shape3D>> shapes = ResourceImporterScene::get_collision_shapes(mesh_node->get_mesh(), e.value.settings);
			const Transform3D transform = ResourceImporterScene::get_collision_shapes_transform(e.value.settings);
			Ref<ArrayMesh> collider_view_mesh;
			collider_view_mesh.instantiate();
			for (Ref<Shape3D> shape : shapes) {
				Ref<ArrayMesh> debug_shape_mesh;
				if (shape.is_valid()) {
					debug_shape_mesh = shape->get_debug_mesh();
				}
				if (debug_shape_mesh.is_valid()) {
					collider_view_mesh->add_surface_from_arrays(
							debug_shape_mesh->surface_get_primitive_type(0),
							debug_shape_mesh->surface_get_arrays(0));
					collider_view_mesh->surface_set_material(
							collider_view_mesh->get_surface_count() - 1,
							collider_mat);
				}
			}
			collider_view->set_mesh(collider_view_mesh);
			collider_view->set_transform(transform);
		}
	}
}
void SceneImportSettings::_update_camera() {