### Godot version

4.0.beta12

### System information

Windows 11, RTX 3080

### Issue description

When a Window Node is created with it's Transparent flag set to true and Project Settings --> Display --> Window --> Subwindows --> Embed Subwindows is false, the Window has a black background. By cycling the transparent flag from false and back to true again, during runtime, the window's background then becomes transparent. 

### Steps to reproduce

Attempt to create a Non-embedded Subwindow with a transparent background using the appropriate flags. 

### Minimal reproduction project

Note: this project is from Reddit user [gongpha](https://www.reddit.com/user/gongpha/) and his Reddit post [Learning a Godot 4.0 Window node](https://www.reddit.com/r/godot/comments/xr8yxn/learning_a_godot_40_window_node/)

https://github.com/gongpha/godot4-window-test
if (!app_focused) {
				if (OS::get_singleton()->get_main_loop()) {
					OS::get_singleton()->get_main_loop()->notification(MainLoop::NOTIFICATION_APPLICATION_FOCUS_IN);
				}
				app_focused = true;
			}
		} break;
		case WM_KILLFOCUS: {
			windows[window_id].window_has_focus = false;
			last_focused_window = window_id;
			
			ReleaseCapture();
			
			for (const KeyValue<int, Vector2> &E : touch_state) {
				_touch_event(window_id, false, E.value.x, E.value.y, E.key);
			}
			touch_state.clear();
			bool self_steal = false;
			HWND new_hwnd = (HWND)wParam;
			if (IsWindow(new_hwnd)) {
				self_steal = true;
			}
			if (!self_steal) {
				if (OS::get_singleton()->get_main_loop()) {
					OS::get_singleton()->get_main_loop()->notification(MainLoop::NOTIFICATION_APPLICATION_FOCUS_OUT);
				}
				app_focused = false;
			}
		} break;
		case WM_ACTIVATE: {