### 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)

} else if (components.size() >= 3 && components[1].begins_with("animation_frame_") && components[1].trim_prefix("animation_frame_").is_valid_int()) {
					int frame = components[1].trim_prefix("animation_frame_").to_int();
					if (frame < 0 || frame >= get_tile_animation_frames_count(coords)) {
						return false;
					}
					if (components[2] == "duration") {
						r_ret = get_tile_animation_frame_duration(coords, frame);
						return true;
					}
					return false;
				} else if (components[1].is_valid_int()) {
					int alternative_id = components[1].to_int();
					if (alternative_id != TileSetSource::INVALID_TILE_ALTERNATIVE && tiles[coords].alternatives.has(alternative_id)) {
						if (components.size() >= 3) {
							bool valid;
							r_ret = tiles[coords].alternatives[alternative_id]->get(components[2], &valid);
							return valid;
						} else {
							
							r_ret = alternative_id;
							return true;
						}
					}
				}
			}
		}
	}
	return false;
}
void TileSetAtlasSource::_get_property_list(List<PropertyInfo> *p_list) const {