### 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)

return navigation_layers.size();
}
void TileSet::add_navigation_layer(int p_index) {
	if (p_index < 0) {
		p_index = navigation_layers.size();
	}
	ERR_FAIL_INDEX(p_index, navigation_layers.size() + 1);
	navigation_layers.insert(p_index, NavigationLayer());
	for (KeyValue<int, Ref<TileSetSource>> source : sources) {
		source.value->add_navigation_layer(p_index);
	}
	notify_property_list_changed();
	emit_changed();
}
void TileSet::move_navigation_layer(int p_from_index, int p_to_pos) {
	ERR_FAIL_INDEX(p_from_index, navigation_layers.size());
	ERR_FAIL_INDEX(p_to_pos, navigation_layers.size() + 1);
	navigation_layers.insert(p_to_pos, navigation_layers[p_from_index]);
	navigation_layers.remove_at(p_to_pos < p_from_index ? p_from_index + 1 : p_from_index);
	for (KeyValue<int, Ref<TileSetSource>> source : sources) {
		source.value->move_navigation_layer(p_from_index, p_to_pos);
	}
	notify_property_list_changed();
	emit_changed();
}
void TileSet::remove_navigation_layer(int p_index) {