### 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)

virtual void remove_navigation_layer(int p_index) override;
	virtual void add_custom_data_layer(int p_index) override;
	virtual void move_custom_data_layer(int p_from_index, int p_to_pos) override;
	virtual void remove_custom_data_layer(int p_index) override;
	virtual void reset_state() override;
	
	void set_texture(Ref<Texture2D> p_texture);
	Ref<Texture2D> get_texture() const;
	void set_margins(Vector2i p_margins);
	Vector2i get_margins() const;
	void set_separation(Vector2i p_separation);
	Vector2i get_separation() const;
	void set_texture_region_size(Vector2i p_tile_size);
	Vector2i get_texture_region_size() const;
	
	void set_use_texture_padding(bool p_use_padding);
	bool get_use_texture_padding() const;
	
	void create_tile(const Vector2i p_atlas_coords, const Vector2i p_size = Vector2i(1, 1));
	void remove_tile(Vector2i p_atlas_coords);
	virtual bool has_tile(Vector2i p_atlas_coords) const override;
	void move_tile_in_atlas(Vector2i p_atlas_coords, Vector2i p_new_atlas_coords = INVALID_ATLAS_COORDS, Vector2i p_new_size = Vector2i(-1, -1));
	Vector2i get_tile_size_in_atlas(Vector2i p_atlas_coords) const;
	virtual int get_tiles_count() const override;
	virtual Vector2i get_tile_id(int p_index) const override;
	bool has_room_for_tile(Vector2i p_atlas_coords, Vector2i p_size, int p_animation_columns, Vector2i p_animation_separation, int p_frames_count, Vector2i p_ignored_tile = INVALID_ATLAS_COORDS) const;
	PackedVector2Array get_tiles_to_be_removed_on_change(Ref<Texture2D> p_texture, Vector2i p_margins, Vector2i p_separation, Vector2i p_texture_region_size);
	Vector2i get_tile_at_coords(Vector2i p_atlas_coords) const;
	
	void set_tile_animation_columns(const Vector2i p_atlas_coords, int p_frame_columns);