### 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)

#endif
				if (is_inside_tree() && collision_animatable && !in_editor) {
					
					last_valid_transform = new_transform;
					set_notify_local_transform(false);
					set_global_transform(new_transform);
					set_notify_local_transform(true);
				}
			} break;
			case TileMap::NOTIFICATION_LOCAL_TRANSFORM_CHANGED: {
				for (Ref<TileMapLayer> &layer : layers) {
					layer->notify_local_xform_changed();
				}
				
				bool in_editor = false;
#ifdef TOOLS_ENABLED
				in_editor = Engine::get_singleton()->is_editor_hint();
#endif
				
				if (is_inside_tree() && !in_editor && collision_animatable) {
					
					set_notify_local_transform(false);
					set_global_transform(last_valid_transform);
					set_notify_local_transform(true);
				}
			} break;
		}
	}
}
void TileMap::queue_update_dirty_quadrants() {