### 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)

ERR_FAIL_COND(!p_tile_set.is_valid());
	ERR_FAIL_COND(!p_tile_set->has_source(p_atlas_source_id));
	ERR_FAIL_COND(!p_tile_set->get_source(p_atlas_source_id)->has_tile(p_atlas_coords));
	ERR_FAIL_COND(!p_tile_set->get_source(p_atlas_source_id)->has_alternative_tile(p_atlas_coords, p_alternative_tile));
	TileSetSource *source = *p_tile_set->get_source(p_atlas_source_id);
	TileSetAtlasSource *atlas_source = Object::cast_to<TileSetAtlasSource>(source);
	if (atlas_source) {
		
		if (p_frame >= 0) {
			ERR_FAIL_INDEX(p_frame, atlas_source->get_tile_animation_frames_count(p_atlas_coords));
		}
		
		Ref<Texture2D> tex = atlas_source->get_runtime_texture();
		if (!tex.is_valid()) {
			return;
		}
		
		Vector2i grid_size = atlas_source->get_atlas_grid_size();
		if (p_atlas_coords.x >= grid_size.x || p_atlas_coords.y >= grid_size.y) {
			return;
		}
		
		const TileData *tile_data = p_tile_data_override ? p_tile_data_override : atlas_source->get_tile_data(p_atlas_coords, p_alternative_tile);
		
		Color modulate = tile_data->get_modulate() * p_modulation;
		
		Vector2 tile_offset = tile_data->get_texture_origin();
		
		Rect2 dest_rect;