### 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)

case TileSet::CELL_NEIGHBOR_TOP_RIGHT_CORNER:
				polygon.push_back(point_list[6]);
				polygon.push_back(point_list[7]);
				polygon.push_back(point_list[8]);
				break;
			case TileSet::CELL_NEIGHBOR_TOP_RIGHT_SIDE:
				polygon.push_back(point_list[5]);
				polygon.push_back(point_list[6]);
				break;
			default:
				break;
		}
	}
	int half_polygon_size = polygon.size();
	for (int i = 0; i < half_polygon_size; i++) {
		polygon.push_back(polygon[half_polygon_size - 1 - i] / 3.0);
	}
	return polygon;
}
Vector<Point2> TileSet::_get_half_offset_corner_terrain_peering_bit_polygon(Vector2i p_size, float p_overlap, TileSet::TileOffsetAxis p_offset_axis, TileSet::CellNeighbor p_bit) {
	Vector<Vector2> point_list = {
		Vector2(3, 0),
		Vector2(3, 3.0 * (1.0 - p_overlap * 2.0)),
		Vector2(1.5, (3.0 * (1.0 - p_overlap * 2.0) + 3.0) / 2.0),
		Vector2(0, 3),
		Vector2(-1.5, (3.0 * (1.0 - p_overlap * 2.0) + 3.0) / 2.0),
		Vector2(-3, 3.0 * (1.0 - p_overlap * 2.0)),
		Vector2(-3, 0),
		Vector2(-3, -3.0 * (1.0 - p_overlap * 2.0)),
		Vector2(-1.5, -(3.0 * (1.0 - p_overlap * 2.0) + 3.0) / 2.0),