### 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
register_create_function("windows", create_func, get_rendering_drivers_func);
}
DisplayServerWindows::~DisplayServerWindows() {
	delete joypad;
	touch_state.clear();
	cursors_cache.clear();
	if (mouse_monitor) {
		UnhookWindowsHookEx(mouse_monitor);
	}
	if (user_proc) {
		SetWindowLongPtr(windows[MAIN_WINDOW_ID].hWnd, GWLP_WNDPROC, (LONG_PTR)user_proc);
	}
	
	screen_set_keep_on(false);
#ifdef GLES3_ENABLED
	
	
#endif
	if (windows.has(MAIN_WINDOW_ID)) {
#ifdef VULKAN_ENABLED
		if (context_vulkan) {
			context_vulkan->window_destroy(MAIN_WINDOW_ID);
		}
#endif
		if (wintab_available && windows[MAIN_WINDOW_ID].wtctx) {
			wintab_WTClose(windows[MAIN_WINDOW_ID].wtctx);