### 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)

set_cell(p_coords, TileSet::INVALID_SOURCE, TileSetSource::INVALID_ATLAS_COORDS, TileSetSource::INVALID_TILE_ALTERNATIVE);
}
int TileMapLayer::get_cell_source_id(const Vector2i &p_coords, bool p_use_proxies) const {
	
	HashMap<Vector2i, TileMapCell>::ConstIterator E = tile_map.find(p_coords);
	if (!E) {
		return TileSet::INVALID_SOURCE;
	}
	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(E->value.source_id, E->value.get_atlas_coords(), E->value.alternative_tile);
		return proxyed[0];
	}
	return E->value.source_id;
}
Vector2i TileMapLayer::get_cell_atlas_coords(const Vector2i &p_coords, bool p_use_proxies) const {
	
	HashMap<Vector2i, TileMapCell>::ConstIterator E = tile_map.find(p_coords);
	if (!E) {
		return TileSetSource::INVALID_ATLAS_COORDS;
	}
	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(E->value.source_id, E->value.get_atlas_coords(), E->value.alternative_tile);
		return proxyed[1];
	}
	return E->value.get_atlas_coords();
}
int TileMapLayer::get_cell_alternative_tile(const Vector2i &p_coords, bool p_use_proxies) const {