### 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)

double picked = Math::random(0.0, sum);
	
	for (const TileMapCell &E : set) {
		if (E.source_id >= 0) {
			Ref<TileSetSource> source = sources[E.source_id];
			Ref<TileSetAtlasSource> atlas_source = source;
			if (atlas_source.is_valid()) {
				TileData *tile_data = atlas_source->get_tile_data(E.get_atlas_coords(), E.alternative_tile);
				count += tile_data->get_probability();
			} else {
				count += 1.0;
			}
		} else {
			count += 1.0;
		}
		if (count >= picked) {
			return E;
		}
	}
	ERR_FAIL_V(TileMapCell());
}
Vector<Vector2> TileSet::get_tile_shape_polygon() {
	Vector<Vector2> points;
	if (tile_shape == TileSet::TILE_SHAPE_SQUARE) {
		points.push_back(Vector2(-0.5, -0.5));
		points.push_back(Vector2(0.5, -0.5));
		points.push_back(Vector2(0.5, 0.5));
		points.push_back(Vector2(-0.5, 0.5));
	} else if (tile_shape == TileSet::TILE_SHAPE_ISOMETRIC) {
		points.push_back(Vector2(0.0, -0.5));