### 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(TileSetSource, Resource);
protected:
	const TileSet *tile_set = nullptr;
	static void _bind_methods();
public:
	static const Vector2i INVALID_ATLAS_COORDS; 
	static const int INVALID_TILE_ALTERNATIVE; 
	
	virtual void set_tile_set(const TileSet *p_tile_set);