### 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)

ERR_FAIL_NULL(NavigationServer2D::get_singleton());
	if (!navigation_map.is_valid()) {
		if (layer_index_in_tile_map_node == 0 && tile_map_node->is_inside_tree()) {
			
			navigation_map = tile_map_node->get_world_2d()->get_navigation_map();
			uses_world_navigation_map = true;
		} else {
			RID new_layer_map = NavigationServer2D::get_singleton()->map_create();
			
			NavigationServer2D::get_singleton()->map_set_cell_size(new_layer_map, 1.0);
			NavigationServer2D::get_singleton()->map_set_active(new_layer_map, true);
			navigation_map = new_layer_map;
			uses_world_navigation_map = false;
		}
	}
}
void TileMapLayer::_navigation_cleanup() {