### 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)

ERR_FAIL_COND_V_MSG(!tiles.has(p_atlas_coords), Rect2i(), vformat("TileSetAtlasSource has no tile at %s.", String(p_atlas_coords)));
	ERR_FAIL_INDEX_V(p_frame, (int)tiles[p_atlas_coords].animation_frames_durations.size(), Rect2i());
	const TileAlternativesData &tad = tiles[p_atlas_coords];
	Vector2i size_in_atlas = tad.size_in_atlas;
	Vector2 region_size = texture_region_size * size_in_atlas + separation * (size_in_atlas - Vector2i(1, 1));
	Vector2i frame_coords = p_atlas_coords + (size_in_atlas + tad.animation_separation) * ((tad.animation_columns > 0) ? Vector2i(p_frame % tad.animation_columns, p_frame / tad.animation_columns) : Vector2i(p_frame, 0));
	Vector2 origin = margins + (frame_coords * (texture_region_size + separation));
	return Rect2(origin, region_size);
}
bool TileSetAtlasSource::is_position_in_tile_texture_region(const Vector2i p_atlas_coords, int p_alternative_tile, Vector2 p_position) const {