### 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)

TerrainConstraint c = TerrainConstraint(tile_map_node, p_coords_array[i], neighbor_list[i], p_terrain);
		c.set_priority(10);
		constraints.insert(c);
	}
	
	for (TerrainConstraint c : _get_terrain_constraints_from_painted_cells_list(painted_set, p_terrain_set, p_ignore_empty_terrains)) {
		constraints.insert(c);
	}
	
	output = terrain_fill_constraints(can_modify_list, p_terrain_set, constraints);
	return output;
}
HashMap<Vector2i, TileSet::TerrainsPattern> TileMapLayer::terrain_fill_pattern(const Vector<Vector2i> &p_coords_array, int p_terrain_set, TileSet::TerrainsPattern p_terrains_pattern, bool p_ignore_empty_terrains) {
	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<Vector2i> can_modify_list;
	RBSet<Vector2i> can_modify_set;
	RBSet<Vector2i> painted_set;
	for (int i = p_coords_array.size() - 1; i >= 0; i--) {
		const Vector2i &coords = p_coords_array[i];
		can_modify_list.push_back(coords);
		can_modify_set.insert(coords);
		painted_set.insert(coords);
	}
	for (Vector2i coords : p_coords_array) {
		
		for (int j = 0; j < TileSet::CELL_NEIGHBOR_MAX; j++) {