### Godot version

4.0 stable

### System information

Windows 10

### Issue description

Running .clear() on a TileMap with Scene tiles leaves the tiles in place, as though nothing happened.

This appears to be the same issue as raised in [#69596](https://github.com/godotengine/godot/issues/69596), [#72456](https://github.com/godotengine/godot/pull/72456), and [67330](https://github.com/godotengine/godot/pull/67330). None of the previous issues seem to have presented a fix for this issue besides running some dummy operations on the TileMap, which have not had any effect for me.

Manually running queue_free() on each tile scene doesn't work, presumably since they are being cached. And running a dummy operation on the TileMap doesn't have any impact to speak of.

Not sure how to proceed, or if it's just impossible to remove Scene tiles once they're created.

### Steps to reproduce

The minimal reproduction project has a TileMap with several simple scene tiles. The attached script attempts to .clear() the TileMap when the user presses Enter, demonstrating my issue.

### Minimal reproduction project

[TileMapMinimumRecreationProject.zip](https://github.com/godotengine/godot/files/10959111/TileMapMinimumRecreationProject.zip)

HashMap<Vector2i, TileSet::TerrainsPattern> output;
	const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	ERR_FAIL_COND_V(!tile_set.is_valid(), output);
	ERR_FAIL_INDEX_V(p_terrain_set, tile_set->get_terrain_sets_count(), output);
	
	Vector<TileSet::CellNeighbor> neighbor_list;
	for (int i = 0; i < p_coords_array.size() - 1; i++) {
		
		TileSet::CellNeighbor found_bit = TileSet::CELL_NEIGHBOR_MAX;
		for (int j = 0; j < TileSet::CELL_NEIGHBOR_MAX; j++) {
			TileSet::CellNeighbor bit = TileSet::CellNeighbor(j);
			if (tile_map_node->is_existing_neighbor(bit)) {
				if (tile_map_node->get_neighbor_cell(p_coords_array[i], bit) == p_coords_array[i + 1]) {
					found_bit = bit;
					break;
				}
			}
		}
		ERR_FAIL_COND_V_MSG(found_bit == TileSet::CELL_NEIGHBOR_MAX, output, vformat("Invalid terrain path, %s is not a neighboring tile of %s", p_coords_array[i + 1], p_coords_array[i]));
		neighbor_list.push_back(found_bit);
	}
	
	Vector<Vector2i> can_modify_list;
	RBSet<Vector2i> can_modify_set;