### 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
_THREAD_SAFE_METHOD_
	ERR_FAIL_COND(!windows.has(p_window));
	ERR_FAIL_INDEX(p_screen, get_screen_count());
	if (window_get_current_screen(p_window) == p_screen) {
		return;
	}
	const WindowData &wd = windows[p_window];
	if (wd.fullscreen) {
		Point2 pos = screen_get_position(p_screen) + _get_screens_origin();
		Size2 size = screen_get_size(p_screen);
		MoveWindow(wd.hWnd, pos.x, pos.y, size.width, size.height, TRUE);
	} else {
		Rect2i srect = screen_get_usable_rect(p_screen);
		Point2i wpos = window_get_position(p_window) - screen_get_position(window_get_current_screen(p_window));
		Size2i wsize = window_get_size(p_window);
		wpos += srect.position;
		wpos.x = CLAMP(wpos.x, srect.position.x, srect.position.x + srect.size.width - wsize.width / 3);
		wpos.y = CLAMP(wpos.y, srect.position.y, srect.position.y + srect.size.height - wsize.height / 3);
		window_set_position(wpos, p_window);
	}
	
	if (mouse_mode == MOUSE_MODE_CONFINED || mouse_mode == MOUSE_MODE_CONFINED_HIDDEN) {
		RECT crect;
		GetClientRect(wd.hWnd, &crect);
		ClientToScreen(wd.hWnd, (POINT *)&crect.left);
		ClientToScreen(wd.hWnd, (POINT *)&crect.right);
		ClipCursor(&crect);
	}
}
Point2i DisplayServerWindows::window_get_position(WindowID p_window) const {