### 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<Image> image = Image::create_empty(size.x, size.y, false, src->get_format());
	for (KeyValue<Vector2i, TileAlternativesData> kv : tiles) {
		for (int frame = 0; frame < (int)kv.value.animation_frames_durations.size(); frame++) {
			
			Rect2i src_rect = get_tile_texture_region(kv.key, frame);
			Rect2i top_src_rect = Rect2i(src_rect.position, Vector2i(src_rect.size.x, 1));
			Rect2i bottom_src_rect = Rect2i(src_rect.position + Vector2i(0, src_rect.size.y - 1), Vector2i(src_rect.size.x, 1));
			Rect2i left_src_rect = Rect2i(src_rect.position, Vector2i(1, src_rect.size.y));
			Rect2i right_src_rect = Rect2i(src_rect.position + Vector2i(src_rect.size.x - 1, 0), Vector2i(1, src_rect.size.y));
			
			Vector2i frame_coords = kv.key + (kv.value.size_in_atlas + kv.value.animation_separation) * ((kv.value.animation_columns > 0) ? Vector2i(frame % kv.value.animation_columns, frame / kv.value.animation_columns) : Vector2i(frame, 0));
			Vector2i base_pos = frame_coords * (texture_region_size + Vector2i(2, 2)) + Vector2i(1, 1);
			image->blit_rect(*src, src_rect, base_pos);
			image->blit_rect(*src, top_src_rect, base_pos + Vector2i(0, -1));
			image->blit_rect(*src, bottom_src_rect, base_pos + Vector2i(0, src_rect.size.y));
			image->blit_rect(*src, left_src_rect, base_pos + Vector2i(-1, 0));
			image->blit_rect(*src, right_src_rect, base_pos + Vector2i(src_rect.size.x, 0));
			image->set_pixelv(base_pos + Vector2i(-1, -1), src->get_pixelv(src_rect.position));
			image->set_pixelv(base_pos + Vector2i(src_rect.size.x, -1), src->get_pixelv(src_rect.position + Vector2i(src_rect.size.x - 1, 0)));
			image->set_pixelv(base_pos + Vector2i(-1, src_rect.size.y), src->get_pixelv(src_rect.position + Vector2i(0, src_rect.size.y - 1)));
			image->set_pixelv(base_pos + Vector2i(src_rect.size.x, src_rect.size.y), src->get_pixelv(src_rect.position + Vector2i(src_rect.size.x - 1, src_rect.size.y - 1)));
		}
	}
	if (!padded_texture.is_valid()) {
		padded_texture.instantiate();
	}
	padded_texture->set_image(image);
	emit_changed();
}
void TileSetScenesCollectionSource::_compute_next_alternative_id() {