### 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<Script> root_script = nullptr;
	if (ScriptServer::is_global_class(root_type)) {
		root_script = ResourceLoader::load(ScriptServer::get_global_class_path(root_type));
		root_type = ScriptServer::get_global_class_base(root_type);
	}
	if (root_type != "Node3D") {
		Node *base_node = Object::cast_to<Node>(ClassDB::instantiate(root_type));
		if (base_node) {
			scene->replace_by(base_node);
			memdelete(scene);
			scene = base_node;
		}
	}
	if (root_script.is_valid()) {
		scene->set_script(Variant(root_script));
	}
	if (p_options["nodes/root_name"] != "Scene Root") {
		scene->set_name(p_options["nodes/root_name"]);
	} else {
		scene->set_name(p_save_path.get_file().get_basename());
	}
	if (!occluder_arrays.first.is_empty() && !occluder_arrays.second.is_empty()) {
		Ref<ArrayOccluder3D> occ = memnew(ArrayOccluder3D);
		occ->set_arrays(occluder_arrays.first, occluder_arrays.second);
		OccluderInstance3D *occluder_instance = memnew(OccluderInstance3D);
		occluder_instance->set_occluder(occ);
		scene->add_child(occluder_instance, true);
		occluder_instance->set_owner(scene);
	}
	bool gen_lods = bool(p_options["meshes/generate_lods"]);