### 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)

break;
		}
	}
	
	if (!is_y_sort_enabled()) {
		for (const Ref<TileMapLayer> &layer : layers) {
			if (layer->is_y_sort_enabled()) {
				warnings.push_back(RTR("A TileMap layer is set as Y-sorted, but Y-sort is not enabled on the TileMap node itself."));
				break;
			}
		}
	}
	
	if (tile_set.is_valid() && tile_set->get_tile_shape() == TileSet::TILE_SHAPE_ISOMETRIC) {
		bool warn = !is_y_sort_enabled();
		if (!warn) {
			for (const Ref<TileMapLayer> &layer : layers) {
				if (!layer->is_y_sort_enabled()) {
					warn = true;
					break;
				}
			}
		}
		if (warn) {
			warnings.push_back(RTR("Isometric TileSet will likely not look as intended without Y-sort enabled for the TileMap and all of its layers."));
		}
	}
	return warnings;
}
void TileMap::_bind_methods() {