### 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)

GDCLASS(TileSetScenesCollectionSource, TileSetSource);
private:
	struct SceneData {
		Ref<PackedScene> scene;
		bool display_placeholder = false;
	};
	Vector<int> scenes_ids;
	HashMap<int, SceneData> scenes;
	int next_scene_id = 1;
	void _compute_next_alternative_id();
protected:
	bool _set(const StringName &p_name, const Variant &p_value);
	bool _get(const StringName &p_name, Variant &r_ret) const;
	void _get_property_list(List<PropertyInfo> *p_list) const;
	static void _bind_methods();
public:
	
	int get_tiles_count() const override;
	Vector2i get_tile_id(int p_tile_index) const override;
	bool has_tile(Vector2i p_atlas_coords) const override;
	
	int get_alternative_tiles_count(const Vector2i p_atlas_coords) const override;
	int get_alternative_tile_id(const Vector2i p_atlas_coords, int p_index) const override;
	bool has_alternative_tile(const Vector2i p_atlas_coords, int p_alternative_tile) const override;
	
	int get_scene_tiles_count() { return get_alternative_tiles_count(Vector2i()); }