### 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)

Vector<String> components = String(p_name).split("/", true, 2);
	if (p_name == "format") {
		if (p_value.get_type() == Variant::INT) {
			format = (TileMapLayer::DataFormat)(p_value.operator int64_t()); 
			return true;
		}
	} else if (p_name == "tile_data") { 
		if (p_value.is_array()) {
			if (layers.size() == 0) {
				Ref<TileMapLayer> new_layer;
				new_layer.instantiate();
				new_layer->set_tile_map(this);
				new_layer->set_layer_index_in_tile_map_node(0);
				layers.push_back(new_layer);
			}
			layers[0]->set_tile_data(format, p_value);
			emit_signal(CoreStringNames::get_singleton()->changed);
			return true;
		}
		return false;
	} else if (components.size() == 2 && components[0].begins_with("layer_") && components[0].trim_prefix("layer_").is_valid_int()) {
		int index = components[0].trim_prefix("layer_").to_int();
		if (index < 0) {
			return false;
		}
		if (index >= (int)layers.size()) {
			_clear_internals();
			while (index >= (int)layers.size()) {