### 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(TileSet, Resource);
#ifndef DISABLE_DEPRECATED
private:
	struct CompatibilityShapeData {
		Vector2i autotile_coords;
		bool one_way;
		float one_way_margin;
		Ref<Shape2D> shape;
		Transform2D transform;
	};
	struct CompatibilityTileData {
		String name;
		Ref<Texture2D> texture;
		Vector2 tex_offset;
		Ref<Material> material;
		Rect2 region;
		int tile_mode = 0;
		Color modulate = Color(1, 1, 1);
		
		int autotile_bitmask_mode = 0;
		Vector2 autotile_icon_coordinate;
		Size2i autotile_tile_size = Size2i(16, 16);