### 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
return mouse_mode;
}
void DisplayServerWindows::warp_mouse(const Point2i &p_position) {
	_THREAD_SAFE_METHOD_
	WindowID window_id = _get_focused_window_or_popup();
	if (!windows.has(window_id)) {
		return; 
	}
	if (mouse_mode == MOUSE_MODE_CAPTURED) {
		old_x = p_position.x;
		old_y = p_position.y;
	} else {
		POINT p;
		p.x = p_position.x;
		p.y = p_position.y;
		ClientToScreen(windows[window_id].hWnd, &p);
		SetCursorPos(p.x, p.y);
	}
}
Point2i DisplayServerWindows::mouse_get_position() const {
	POINT p;
	GetCursorPos(&p);
	return Point2i(p.x, p.y) - _get_screens_origin();
}
BitField<MouseButtonMask> DisplayServerWindows::mouse_get_button_state() const {
	return last_button_state;
}
void DisplayServerWindows::clipboard_set(const String &p_text) {