### 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)

#ifndef TILE_SET_H
#define TILE_SET_H
#include "core/io/resource.h"
#include "core/object/object.h"
#include "core/templates/local_vector.h"
#include "core/templates/rb_set.h"
#include "scene/2d/light_occluder_2d.h"
#include "scene/main/canvas_item.h"
#include "scene/resources/concave_polygon_shape_2d.h"
#include "scene/resources/convex_polygon_shape_2d.h"
#include "scene/resources/navigation_polygon.h"
#include "scene/resources/packed_scene.h"
#include "scene/resources/physics_material.h"
#include "scene/resources/shape_2d.h"
#ifndef DISABLE_DEPRECATED
#include "scene/resources/shader.h"
#include "scene/resources/texture.h"
#endif
class TileMap;