### Godot version

4.01

### System information

Windows 10

### Issue description

It seems a tiles Custom Data is cleared/not set when "Local to Scene" is enabled for the TileMap in the Resource section. At least the custom data isn't set by the time of the _ready function in the script attached to the TileMap.

### Steps to reproduce

create TileMap and tileset with custom data and attached script. in _ready method attempt to read custom data from a used cell. 

In Attached project run it. It will print_debug if it found custom data or not. "Local to Scene" is enabled so it will not find the custom data.

### Minimal reproduction project

[TileMapCustomDataLocalBugReproduce.zip](https://github.com/godotengine/godot/files/11470771/TileMapCustomDataLocalBugReproduce.zip)

ERR_FAIL_COND(!scenes.has(p_id));
	if (p_packed_scene.is_valid()) {
		
		Ref<SceneState> scene_state = p_packed_scene->get_state();
		String type;
		while (scene_state.is_valid() && type.is_empty()) {
			
			ERR_FAIL_COND(scene_state->get_node_count() < 1);
			type = scene_state->get_node_type(0);
			scene_state = scene_state->get_base_scene_state();
		}
		ERR_FAIL_COND_MSG(type.is_empty(), vformat("Invalid PackedScene for TileSetScenesCollectionSource: %s. Could not get the type of the root node.", p_packed_scene->get_path()));
		bool extends_correct_class = ClassDB::is_parent_class(type, "CanvasItem");
		ERR_FAIL_COND_MSG(!extends_correct_class, vformat("Invalid PackedScene for TileSetScenesCollectionSource: %s. Root node should extend CanvasItem. Found %s instead.", p_packed_scene->get_path(), type));
		scenes[p_id].scene = p_packed_scene;
	} else {
		scenes[p_id].scene = Ref<PackedScene>();
	}
	emit_signal(SNAME("changed"));
}
Ref<PackedScene> TileSetScenesCollectionSource::get_scene_tile_scene(int p_id) const {