### 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)

}
	}
	if (bool(p_options["skins/use_named_skins"])) {
		import_flags |= EditorSceneFormatImporter::IMPORT_USE_NAMED_SKIN_BINDS;
	}
	bool ensure_tangents = p_options["meshes/ensure_tangents"];
	if (ensure_tangents) {
		import_flags |= EditorSceneFormatImporter::IMPORT_GENERATE_TANGENT_ARRAYS;
	}
	Error err = OK;
	List<String> missing_deps; 
	Node *scene = importer->import_scene(src_path, import_flags, p_options, &missing_deps, &err);
	if (!scene || err != OK) {
		return err;
	}
	bool apply_root = true;
	if (p_options.has("nodes/apply_root_scale")) {
		apply_root = p_options["nodes/apply_root_scale"];
	}
	real_t root_scale = 1;
	if (p_options.has("nodes/root_scale")) {
		root_scale = p_options["nodes/root_scale"];
	}
	if (Object::cast_to<Node3D>(scene)) {
		Object::cast_to<Node3D>(scene)->scale(Vector3(root_scale, root_scale, root_scale));
	}
	if (apply_root) {
		_apply_permanent_rotation_scale_to_node(scene);
		Object::cast_to<Node3D>(scene)->scale(Vector3(root_scale, root_scale, root_scale).inverse());
	}