### 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)

}
				return false;
			} else if (components[1].is_valid_int()) {
				int alternative_id = components[1].to_int();
				if (alternative_id != TileSetSource::INVALID_TILE_ALTERNATIVE) {
					
					if (!has_alternative_tile(coords, alternative_id)) {
						create_alternative_tile(coords, alternative_id);
					}
					if (!tiles[coords].alternatives.has(alternative_id)) {
						tiles[coords].alternatives[alternative_id] = memnew(TileData);
						tiles[coords].alternatives[alternative_id]->set_tile_set(tile_set);
						tiles[coords].alternatives[alternative_id]->set_allow_transform(alternative_id > 0);
						tiles[coords].alternatives_ids.push_back(alternative_id);
					}
					if (components.size() >= 3) {
						bool valid;
						tiles[coords].alternatives[alternative_id]->set(components[2], p_value, &valid);
						return valid;
					} else {
						
						return true;
					}
				}
			}
		}
	}
	return false;
}
bool TileSetAtlasSource::_get(const StringName &p_name, Variant &r_ret) const {