### 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)

Ref<PhysicsMaterial> physics_material;
	};
	Vector<PhysicsLayer> physics_layers;
	
	struct Terrain {
		String name;
		Color color;
	};
	struct TerrainSet {
		TerrainMode mode = TERRAIN_MODE_MATCH_CORNERS_AND_SIDES;
		Vector<Terrain> terrains;
	};
	Vector<TerrainSet> terrain_sets;
	HashMap<TerrainMode, Ref<ArrayMesh>> terrain_meshes;
	HashMap<TerrainMode, HashMap<CellNeighbor, Ref<ArrayMesh>>> terrain_peering_bits_meshes;
	bool terrain_bits_meshes_dirty = true;
	LocalVector<RBMap<TileSet::TerrainsPattern, RBSet<TileMapCell>>> per_terrain_pattern_tiles; 
	bool terrains_cache_dirty = true;
	void _update_terrains_cache();
	
	struct NavigationLayer {
		uint32_t layers = 1;
	};
	Vector<NavigationLayer> navigation_layers;
	
	struct CustomDataLayer {
		String name;
		Variant::Type type = Variant::NIL;
	};
	Vector<CustomDataLayer> custom_data_layers;