### 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 (convex_shape.is_valid()) {
										Vector<Vector2> polygon = convex_shape->get_points();
										for (int point_index = 0; point_index < polygon.size(); point_index++) {
											polygon.write[point_index] = xform.xform(csd.transform.xform(polygon[point_index]) - ctd->autotile_tile_size / 2.0);
										}
										tile_data->set_collision_polygons_count(0, tile_data->get_collision_polygons_count(0) + 1);
										int index = tile_data->get_collision_polygons_count(0) - 1;
										tile_data->set_collision_polygon_one_way(0, index, csd.one_way);
										tile_data->set_collision_polygon_one_way_margin(0, index, csd.one_way_margin);
										tile_data->set_collision_polygon_points(0, index, polygon);
									}
								}
							}
							
							
							
							
							
							
							
							
						}
					}
				}
				
				if (!compatibility_size_count.has(ctd->region.get_size())) {
					compatibility_size_count[ctd->autotile_tile_size] = 0;
				}
				compatibility_size_count[ctd->autotile_tile_size] += atlas_size.x * atlas_size.y;
			} break;