### 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)

Ref<EditorSceneFormatImporter> importer;
	String ext = p_source_file.get_extension().to_lower();
	EditorProgress progress("pre-import", TTR("Pre-Import Scene"), 0);
	progress.step(TTR("Importing Scene..."), 0);
	for (Ref<EditorSceneFormatImporter> importer_elem : importers) {
		List<String> extensions;
		importer_elem->get_extensions(&extensions);
		for (const String &F : extensions) {
			if (F.to_lower() == ext) {
				importer = importer_elem;
				break;
			}
		}
		if (importer.is_valid()) {
			break;
		}
	}
	ERR_FAIL_COND_V(!importer.is_valid(), nullptr);
	Error err = OK;
	Node *scene = importer->import_scene(p_source_file, EditorSceneFormatImporter::IMPORT_ANIMATION | EditorSceneFormatImporter::IMPORT_GENERATE_TANGENT_ARRAYS, p_options, nullptr, &err);
	if (!scene || err != OK) {
		return nullptr;
	}
	HashMap<Ref<ImporterMesh>, Vector<Ref<Shape3D>>> collision_map;
	List<Pair<NodePath, Node *>> node_renames;
	_pre_fix_node(scene, scene, collision_map, nullptr, node_renames);
	return scene;
}
Error ResourceImporterScene::import(const String &p_source_file, const String &p_save_path, const HashMap<StringName, Variant> &p_options, List<String> *r_platform_variants, List<String> *r_gen_files, Variant *r_metadata) {