### 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)

Vector<Ref<OccluderPolygon2D>> occluders;
	
	struct PhysicsLayerTileData {
		struct PolygonShapeTileData {
			LocalVector<Vector2> polygon;
			LocalVector<Ref<ConvexPolygonShape2D>> shapes;
			bool one_way = false;
			float one_way_margin = 1.0;
		};
		Vector2 linear_velocity;
		double angular_velocity = 0.0;
		Vector<PolygonShapeTileData> polygons;
	};
	Vector<PhysicsLayerTileData> physics;
	
	
	int terrain_set = -1;
	int terrain = -1;
	int terrain_peering_bits[16] = { -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1 };
	
	Vector<Ref<NavigationPolygon>> navigation;
	
	double probability = 1.0;
	
	Vector<Variant> custom_data;
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();