### 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
}
#define MI_WP_SIGNATURE 0xFF515700
#define SIGNATURE_MASK 0xFFFFFF00
#define IsPenEvent(dw) (((dw)&SIGNATURE_MASK) == MI_WP_SIGNATURE)
#define IsTouchEvent(dw) (IsPenEvent(dw) && ((dw)&0x80))
void DisplayServerWindows::_touch_event(WindowID p_window, bool p_pressed, float p_x, float p_y, int idx) {
	if (touch_state.has(idx) == p_pressed) {
		return;
	}
	if (p_pressed) {
		touch_state.insert(idx, Vector2(p_x, p_y));
	} else {
		touch_state.erase(idx);
	}
	Ref<InputEventScreenTouch> event;
	event.instantiate();
	event->set_index(idx);
	event->set_window_id(p_window);
	event->set_pressed(p_pressed);
	event->set_position(Vector2(p_x, p_y));
	Input::get_singleton()->parse_input_event(event);
}
void DisplayServerWindows::_drag_event(WindowID p_window, float p_x, float p_y, int idx) {