### 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)

List<ImportOption> iopts;
								get_internal_import_options(INTERNAL_IMPORT_CATEGORY_MATERIAL, &iopts);
								for (const ImportOption &E : iopts) {
									if (!matdata.has(E.option.name)) {
										matdata[E.option.name] = E.default_value;
									}
								}
							}
							for (int j = 0; j < post_importer_plugins.size(); j++) {
								post_importer_plugins.write[j]->internal_process(EditorScenePostImportPlugin::INTERNAL_IMPORT_CATEGORY_MATERIAL, p_root, p_node, mat, matdata);
							}
							if (matdata.has("use_external/enabled") && bool(matdata["use_external/enabled"]) && matdata.has("use_external/path")) {
								String path = matdata["use_external/path"];
								Ref<Material> external_mat = ResourceLoader::load(path);
								if (external_mat.is_valid()) {
									m->set_surface_material(i, external_mat);
								}
							}
						}
					}
				}
				r_scanned_meshes.insert(m);
			}
			if (node_settings.has("generate/physics")) {
				int mesh_physics_mode = MeshPhysicsMode::MESH_PHYSICS_DISABLED;
				const bool generate_collider = node_settings["generate/physics"];
				if (generate_collider) {
					mesh_physics_mode = MeshPhysicsMode::MESH_PHYSICS_MESH_AND_STATIC_COLLIDER;
					if (node_settings.has("physics/body_type")) {