### 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
Callable callable = windows[E->get()].input_event_callback;
				if (callable.is_valid()) {
					callable.callp((const Variant **)&evp, 1, ret, ce);
				}
			}
			in_dispatch_input_event = false;
			return;
		}
	}
	Ref<InputEventFromWindow> event_from_window = p_event;
	if (event_from_window.is_valid() && event_from_window->get_window_id() != INVALID_WINDOW_ID) {
		
		if (windows.has(event_from_window->get_window_id())) {
			Callable callable = windows[event_from_window->get_window_id()].input_event_callback;
			if (callable.is_valid()) {
				callable.callp((const Variant **)&evp, 1, ret, ce);
			}
		}
	} else {
		
		for (const KeyValue<WindowID, WindowData> &E : windows) {
			const Callable callable = E.value.input_event_callback;
			if (callable.is_valid()) {
				callable.callp((const Variant **)&evp, 1, ret, ce);
			}
		}
	}
	in_dispatch_input_event = false;
}
LRESULT CALLBACK MouseProc(int code, WPARAM wParam, LPARAM lParam) {