### 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)

TypedArray<Vector2i> a;
	a.resize(tile_map.size());
	int i = 0;
	for (const KeyValue<Vector2i, TileMapCell> &E : tile_map) {
		Vector2i p(E.key.x, E.key.y);
		a[i++] = p;
	}
	return a;
}
TypedArray<Vector2i> TileMapLayer::get_used_cells_by_id(int p_source_id, const Vector2i p_atlas_coords, int p_alternative_tile) const {
	
	TypedArray<Vector2i> a;
	for (const KeyValue<Vector2i, TileMapCell> &E : tile_map) {
		if ((p_source_id == TileSet::INVALID_SOURCE || p_source_id == E.value.source_id) &&
				(p_atlas_coords == TileSetSource::INVALID_ATLAS_COORDS || p_atlas_coords == E.value.get_atlas_coords()) &&
				(p_alternative_tile == TileSetSource::INVALID_TILE_ALTERNATIVE || p_alternative_tile == E.value.alternative_tile)) {
			a.push_back(E.key);
		}
	}
	return a;
}
Rect2i TileMapLayer::get_used_rect() const {