### 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)

int ret;
	if (GDVIRTUAL_CALL(_get_import_flags, ret)) {
		return ret;
	}
	ERR_FAIL_V(0);
}
void EditorSceneFormatImporter::get_extensions(List<String> *r_extensions) const {
	Vector<String> arr;
	if (GDVIRTUAL_CALL(_get_extensions, arr)) {
		for (int i = 0; i < arr.size(); i++) {
			r_extensions->push_back(arr[i]);
		}
		return;
	}
	ERR_FAIL();
}
Node *EditorSceneFormatImporter::import_scene(const String &p_path, uint32_t p_flags, const HashMap<StringName, Variant> &p_options, List<String> *r_missing_deps, Error *r_err) {
	Dictionary options_dict;
	for (const KeyValue<StringName, Variant> &elem : p_options) {
		options_dict[elem.key] = elem.value;
	}
	Object *ret = nullptr;
	if (GDVIRTUAL_CALL(_import_scene, p_path, p_flags, options_dict, ret)) {
		return Object::cast_to<Node>(ret);
	}
	ERR_FAIL_V(nullptr);
}
void EditorSceneFormatImporter::get_import_options(const String &p_path, List<ResourceImporter::ImportOption> *r_options) {