### 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_BOTTOM_CORNER:
			polygon.push_back(Vector2(-0.5, 0.5) * unit);
			polygon.push_back(Vector2(-1.5, 1.5) * unit);
			polygon.push_back(Vector2(0, 3) * unit);
			polygon.push_back(Vector2(1.5, 1.5) * unit);
			polygon.push_back(Vector2(0.5, 0.5) * unit);
			polygon.push_back(Vector2(0, 1) * unit);
			break;
		case TileSet::CELL_NEIGHBOR_LEFT_CORNER:
			polygon.push_back(Vector2(-0.5, -0.5) * unit);
			polygon.push_back(Vector2(-1.5, -1.5) * unit);
			polygon.push_back(Vector2(-3, 0) * unit);
			polygon.push_back(Vector2(-1.5, 1.5) * unit);
			polygon.push_back(Vector2(-0.5, 0.5) * unit);
			polygon.push_back(Vector2(-1, 0) * unit);
			break;
		case TileSet::CELL_NEIGHBOR_TOP_CORNER:
			polygon.push_back(Vector2(-0.5, -0.5) * unit);
			polygon.push_back(Vector2(-1.5, -1.5) * unit);
			polygon.push_back(Vector2(0, -3) * unit);
			polygon.push_back(Vector2(1.5, -1.5) * unit);
			polygon.push_back(Vector2(0.5, -0.5) * unit);
			polygon.push_back(Vector2(0, -1) * unit);
			break;
		default:
			break;
	}
	return polygon;
}
Vector<Point2> TileSet::_get_isometric_side_terrain_peering_bit_polygon(Vector2i p_size, TileSet::CellNeighbor p_bit) {