### 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)

bool has_alternative_level_tile_proxy(int p_source_from, Vector2i p_coords_from, int p_alternative_from);
	void remove_alternative_level_tile_proxy(int p_source_from, Vector2i p_coords_from, int p_alternative_from);
	Array get_source_level_tile_proxies() const;
	Array get_coords_level_tile_proxies() const;
	Array get_alternative_level_tile_proxies() const;
	Array map_tile_proxy(int p_source_from, Vector2i p_coords_from, int p_alternative_from) const;
	void cleanup_invalid_tile_proxies();
	void clear_tile_proxies();
	
	int add_pattern(Ref<TileMapPattern> p_pattern, int p_index = -1);
	Ref<TileMapPattern> get_pattern(int p_index);
	void remove_pattern(int p_index);
	int get_patterns_count();
	
	RBSet<TerrainsPattern> get_terrains_pattern_set(int p_terrain_set);
	RBSet<TileMapCell> get_tiles_for_terrains_pattern(int p_terrain_set, TerrainsPattern p_terrain_tile_pattern);
	TileMapCell get_random_tile_from_terrains_pattern(int p_terrain_set, TerrainsPattern p_terrain_tile_pattern);
	
	Vector<Vector2> get_tile_shape_polygon();
	void draw_tile_shape(CanvasItem *p_canvas_item, Transform2D p_transform, Color p_color, bool p_filled = false, Ref<Texture2D> p_texture = Ref<Texture2D>());
	Vector<Point2> get_terrain_polygon(int p_terrain_set);
	Vector<Point2> get_terrain_peering_bit_polygon(int p_terrain_set, TileSet::CellNeighbor p_bit);
	void draw_terrains(CanvasItem *p_canvas_item, Transform2D p_transform, const TileData *p_tile_data);
	Vector<Vector<Ref<Texture2D>>> generate_terrains_icons(Size2i p_size);
	
	virtual void reset_state() override;
	TileSet();
	~TileSet();
};
class TileSetSource : public Resource {