### 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)

if (!tile_map.has(p_coords)) {
		return TileMapCell();
	} else {
		TileMapCell c = tile_map.find(p_coords)->value;
		const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
		if (p_use_proxies && tile_set.is_valid()) {
			Array proxyed = tile_set->map_tile_proxy(c.source_id, c.get_atlas_coords(), c.alternative_tile);
			c.source_id = proxyed[0];
			c.set_atlas_coords(proxyed[1]);
			c.alternative_tile = proxyed[2];
		}
		return c;
	}
}
int TileMapLayer::get_effective_quadrant_size() const {
	
	if (tile_map_node->is_y_sort_enabled() && is_y_sort_enabled()) {
		return 1;
	} else {
		return tile_map_node->get_quadrant_size();
	}
}
void TileMapLayer::set_tile_data(TileMapLayer::DataFormat p_format, const Vector<int> &p_data) {