### 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)

layer_index_in_tile_map_node = p_index;
}
Rect2 TileMapLayer::get_rect(bool &r_changed) const {
	
	r_changed = false;
#ifdef DEBUG_ENABLED
	if (rect_cache_dirty) {
		Rect2 r_total;
		bool first = true;
		for (const KeyValue<Vector2i, TileMapQuadrant> &E : quadrant_map) {
			Rect2 r;
			r.position = tile_map_node->map_to_local(E.key * get_effective_quadrant_size());
			r.expand_to(tile_map_node->map_to_local((E.key + Vector2i(1, 0)) * get_effective_quadrant_size()));
			r.expand_to(tile_map_node->map_to_local((E.key + Vector2i(1, 1)) * get_effective_quadrant_size()));
			r.expand_to(tile_map_node->map_to_local((E.key + Vector2i(0, 1)) * get_effective_quadrant_size()));
			if (first) {
				r_total = r;
				first = false;
			} else {
				r_total = r_total.merge(r);
			}
		}
		r_changed = rect_cache != r_total;
		rect_cache = r_total;
		rect_cache_dirty = false;
	}
#endif
	return rect_cache;
}
HashMap<Vector2i, TileSet::TerrainsPattern> TileMapLayer::terrain_fill_constraints(const Vector<Vector2i> &p_to_replace, int p_terrain_set, const RBSet<TerrainConstraint> &p_constraints) {