### 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)

ERR_FAIL_INDEX_V(p_terrain_set, terrain_sets.size(), RBSet<TileMapCell>());
	_update_terrains_cache();
	return per_terrain_pattern_tiles[p_terrain_set][p_terrain_tile_pattern];
}
TileMapCell TileSet::get_random_tile_from_terrains_pattern(int p_terrain_set, TileSet::TerrainsPattern p_terrain_tile_pattern) {
	ERR_FAIL_INDEX_V(p_terrain_set, terrain_sets.size(), TileMapCell());
	_update_terrains_cache();
	
	double sum = 0.0;
	RBSet<TileMapCell> set = per_terrain_pattern_tiles[p_terrain_set][p_terrain_tile_pattern];
	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);
				sum += tile_data->get_probability();
			} else {
				sum += 1.0;
			}
		} else {
			sum += 1.0;
		}
	}
	
	double count = 0.0;