### 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)

polygon.push_back(point_list[17]);
				polygon.push_back(point_list[0]);
				break;
			case TileSet::CELL_NEIGHBOR_BOTTOM_LEFT_CORNER:
				polygon.push_back(point_list[15]);
				polygon.push_back(point_list[16]);
				polygon.push_back(point_list[17]);
				break;
			case TileSet::CELL_NEIGHBOR_BOTTOM_LEFT_SIDE:
				polygon.push_back(point_list[14]);
				polygon.push_back(point_list[15]);
				break;
			case TileSet::CELL_NEIGHBOR_LEFT_CORNER:
				polygon.push_back(point_list[12]);
				polygon.push_back(point_list[13]);
				polygon.push_back(point_list[14]);
				break;
			case TileSet::CELL_NEIGHBOR_TOP_LEFT_SIDE:
				polygon.push_back(point_list[11]);
				polygon.push_back(point_list[12]);
				break;
			case TileSet::CELL_NEIGHBOR_TOP_LEFT_CORNER:
				polygon.push_back(point_list[9]);
				polygon.push_back(point_list[10]);
				polygon.push_back(point_list[11]);
				break;
			case TileSet::CELL_NEIGHBOR_TOP_SIDE:
				polygon.push_back(point_list[8]);
				polygon.push_back(point_list[9]);
				break;