### 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)

tile_shape = p_shape;
	for (KeyValue<int, Ref<TileSetSource>> &E_source : sources) {
		E_source.value->notify_tile_data_properties_should_change();
	}
	terrain_bits_meshes_dirty = true;
	tile_meshes_dirty = true;
	notify_property_list_changed();
	emit_changed();
}
TileSet::TileShape TileSet::get_tile_shape() const {
	return tile_shape;
}
void TileSet::set_tile_layout(TileSet::TileLayout p_layout) {