### 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_INDEX_V(p_index, tiles_ids.size(), TileSetSource::INVALID_ATLAS_COORDS);
	return tiles_ids[p_index];
}
bool TileSetAtlasSource::has_room_for_tile(Vector2i p_atlas_coords, Vector2i p_size, int p_animation_columns, Vector2i p_animation_separation, int p_frames_count, Vector2i p_ignored_tile) const {
	if (p_atlas_coords.x < 0 || p_atlas_coords.y < 0) {
		return false;
	}
	if (p_size.x <= 0 || p_size.y <= 0) {
		return false;
	}
	Size2i atlas_grid_size = get_atlas_grid_size();
	for (int frame = 0; frame < p_frames_count; frame++) {
		Vector2i frame_coords = p_atlas_coords + (p_size + p_animation_separation) * ((p_animation_columns > 0) ? Vector2i(frame % p_animation_columns, frame / p_animation_columns) : Vector2i(frame, 0));
		for (int x = 0; x < p_size.x; x++) {
			for (int y = 0; y < p_size.y; y++) {
				Vector2i coords = frame_coords + Vector2i(x, y);
				if (_coords_mapping_cache.has(coords) && _coords_mapping_cache[coords] != p_ignored_tile) {
					return false;
				}
				if (coords.x >= atlas_grid_size.x || coords.y >= atlas_grid_size.y) {
					return false;
				}
			}
		}
	}
	return true;
}
PackedVector2Array TileSetAtlasSource::get_tiles_to_be_removed_on_change(Ref<Texture2D> p_texture, Vector2i p_margins, Vector2i p_separation, Vector2i p_texture_region_size) {