### 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)

return Vector2i(coord_x, coord_y);
	}
	void set_atlas_coords(const Vector2i &r_coords) {
		coord_x = r_coords.x;
		coord_y = r_coords.y;
	}
	bool operator<(const TileMapCell &p_other) const {
		if (source_id == p_other.source_id) {
			if (coord_x == p_other.coord_x) {
				if (coord_y == p_other.coord_y) {
					return alternative_tile < p_other.alternative_tile;
				} else {
					return coord_y < p_other.coord_y;
				}
			} else {
				return coord_x < p_other.coord_x;
			}
		} else {
			return source_id < p_other.source_id;
		}
	}
	bool operator!=(const TileMapCell &p_other) const {
		return !(source_id == p_other.source_id && coord_x == p_other.coord_x && coord_y == p_other.coord_y && alternative_tile == p_other.alternative_tile);
	}
	bool operator==(const TileMapCell &p_other) const {
		return source_id == p_other.source_id && coord_x == p_other.coord_x && coord_y == p_other.coord_y && alternative_tile == p_other.alternative_tile;
	}
};
class TileMapPattern : public Resource {