### 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
WindowRect.right = screen_rect.position.x + screen_rect.size.x;
		WindowRect.top = screen_rect.position.y;
		WindowRect.bottom = screen_rect.position.y + screen_rect.size.y;
	} else {
		Rect2i srect = screen_get_usable_rect(rq_screen);
		Point2i wpos = p_rect.position;
		if (srect != Rect2i()) {
			wpos.x = CLAMP(wpos.x, srect.position.x, srect.position.x + srect.size.width - p_rect.size.width / 3);
			wpos.y = CLAMP(wpos.y, srect.position.y, srect.position.y + srect.size.height - p_rect.size.height / 3);
		}
		WindowRect.left = wpos.x;
		WindowRect.right = wpos.x + p_rect.size.x;
		WindowRect.top = wpos.y;
		WindowRect.bottom = wpos.y + p_rect.size.y;
	}
	Point2i offset = _get_screens_origin();
	WindowRect.left += offset.x;
	WindowRect.right += offset.x;
	WindowRect.top += offset.y;
	WindowRect.bottom += offset.y;
	AdjustWindowRectEx(&WindowRect, dwStyle, FALSE, dwExStyle);
	WindowID id = window_id_counter;
	{
		WindowData &wd = windows[id];
		wd.hWnd = CreateWindowExW(
				dwExStyle,
				L"Engine", L"",
				dwStyle,