### 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(p_terrain_set, terrain_sets.size());
	Vector<Terrain> &terrains = terrain_sets.write[p_terrain_set].terrains;
	ERR_FAIL_INDEX(p_from_index, terrains.size());
	ERR_FAIL_INDEX(p_to_pos, terrains.size() + 1);
	terrains.insert(p_to_pos, terrains[p_from_index]);
	terrains.remove_at(p_to_pos < p_from_index ? p_from_index + 1 : p_from_index);
	for (KeyValue<int, Ref<TileSetSource>> source : sources) {
		source.value->move_terrain(p_terrain_set, p_from_index, p_to_pos);
	}
	notify_property_list_changed();
	terrains_cache_dirty = true;
	emit_changed();
}
void TileSet::remove_terrain(int p_terrain_set, int p_index) {
	ERR_FAIL_INDEX(p_terrain_set, terrain_sets.size());
	Vector<Terrain> &terrains = terrain_sets.write[p_terrain_set].terrains;
	ERR_FAIL_INDEX(p_index, terrains.size());
	terrains.remove_at(p_index);
	for (KeyValue<int, Ref<TileSetSource>> source : sources) {
		source.value->remove_terrain(p_terrain_set, p_index);
	}
	notify_property_list_changed();
	terrains_cache_dirty = true;
	emit_changed();
}
void TileSet::set_terrain_name(int p_terrain_set, int p_terrain_index, String p_name) {