### 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(), TileSet::TERRAIN_MODE_MATCH_CORNERS_AND_SIDES);
	return terrain_sets[p_terrain_set].mode;
}
int TileSet::get_terrains_count(int p_terrain_set) const {
	ERR_FAIL_INDEX_V(p_terrain_set, terrain_sets.size(), -1);
	return terrain_sets[p_terrain_set].terrains.size();
}
void TileSet::add_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;
	if (p_index < 0) {
		p_index = terrains.size();
	}
	ERR_FAIL_INDEX(p_index, terrains.size() + 1);
	terrains.insert(p_index, Terrain());
	
	float hue_rotate = (terrains.size() % 16) / 16.0;
	Color c;
	c.set_hsv(Math::fmod(float(hue_rotate), float(1.0)), 0.5, 0.5);
	terrains.write[p_index].color = c;
	terrains.write[p_index].name = String(vformat("Terrain %d", p_index));
	for (KeyValue<int, Ref<TileSetSource>> source : sources) {
		source.value->add_terrain(p_terrain_set, p_index);
	}
	notify_property_list_changed();
	terrains_cache_dirty = true;
	emit_changed();
}
void TileSet::move_terrain(int p_terrain_set, int p_from_index, int p_to_pos) {