### 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)

DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_BOTTOM_LEFT_SIDE, 2, 3);
				DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_LEFT_SIDE, 1, 2);
				DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_TOP_LEFT_SIDE, 0, 1);
				DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_TOP_RIGHT_SIDE, 5, 0);
				DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_RIGHT_SIDE, 4, 5);
			} else {
				DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_BOTTOM_RIGHT_SIDE, 3, 4);
				DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_BOTTOM_SIDE, 4, 5);
				DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_BOTTOM_LEFT_SIDE, 5, 0);
				DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_TOP_LEFT_SIDE, 0, 1);
				DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_TOP_SIDE, 1, 2);
				DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_TOP_RIGHT_SIDE, 2, 3);
			}
		}
	}
#undef DRAW_SIDE_IF_NEEDED
}
PackedStringArray TileMap::get_configuration_warnings() const {
	PackedStringArray warnings = Node::get_configuration_warnings();
	
	RBSet<int> y_sorted_z_index;
	for (const Ref<TileMapLayer> &layer : layers) {
		if (layer->is_y_sort_enabled()) {
			y_sorted_z_index.insert(layer->get_z_index());
		}
	}
	
	for (const Ref<TileMapLayer> &layer : layers) {
		if (!layer->is_y_sort_enabled() && y_sorted_z_index.has(layer->get_z_index())) {
			warnings.push_back(RTR("A Y-sorted layer has the same Z-index value as a not Y-sorted layer.\nThis may lead to unwanted behaviors, as a layer that is not Y-sorted will be Y-sorted as a whole with tiles from Y-sorted layers."));