### 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)

}
				if (polygon_index >= physics[layer_index].polygons.size()) {
					physics.write[layer_index].polygons.resize(polygon_index + 1);
				}
			}
			if (components[2] == "points") {
				Vector<Vector2> polygon = p_value;
				set_collision_polygon_points(layer_index, polygon_index, polygon);
				return true;
			} else if (components[2] == "one_way") {
				set_collision_polygon_one_way(layer_index, polygon_index, p_value);
				return true;
			} else if (components[2] == "one_way_margin") {
				set_collision_polygon_one_way_margin(layer_index, polygon_index, p_value);
				return true;
			}
		}
	} else if (components.size() == 2 && components[0].begins_with("navigation_layer_") && components[0].trim_prefix("navigation_layer_").is_valid_int()) {
		
		int layer_index = components[0].trim_prefix("navigation_layer_").to_int();
		ERR_FAIL_COND_V(layer_index < 0, false);
		if (components[1] == "polygon") {
			Ref<NavigationPolygon> polygon = p_value;
			if (layer_index >= navigation.size()) {
				if (tile_set) {
					return false;
				} else {
					navigation.resize(layer_index + 1);
				}
			}