### 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)

ERR_FAIL_COND(p_plugin.is_null());
	if (p_first_priority) {
		post_importer_plugins.insert(0, p_plugin);
	} else {
		post_importer_plugins.push_back(p_plugin);
	}
}
void ResourceImporterScene::remove_importer(Ref<EditorSceneFormatImporter> p_importer) {
	importers.erase(p_importer);
}
void ResourceImporterScene::clean_up_importer_plugins() {
	importers.clear();
	post_importer_plugins.clear();
}
uint32_t EditorSceneFormatImporterESCN::get_import_flags() const {
	return IMPORT_SCENE;
}
void EditorSceneFormatImporterESCN::get_extensions(List<String> *r_extensions) const {
	r_extensions->push_back("escn");
}
Node *EditorSceneFormatImporterESCN::import_scene(const String &p_path, uint32_t p_flags, const HashMap<StringName, Variant> &p_options, List<String> *r_missing_deps, Error *r_err) {
	Error error;
	Ref<PackedScene> ps = ResourceFormatLoaderText::singleton->load(p_path, p_path, &error);
	ERR_FAIL_COND_V_MSG(!ps.is_valid(), nullptr, "Cannot load scene as text resource from path '" + p_path + "'.");
	Node *scene = ps->instantiate();
	ERR_FAIL_COND_V(!scene, nullptr);
	return scene;
}