### 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));
	WindowData &wd = windows[p_window];
	if (wd.fullscreen || wd.maximized) {
		return;
	}
	Point2i offset = _get_screens_origin();
	RECT rc;
	rc.left = p_position.x + offset.x;
	rc.right = p_position.x + wd.width + offset.x;
	rc.bottom = p_position.y + wd.height + offset.y;
	rc.top = p_position.y + offset.y;
	const DWORD style = GetWindowLongPtr(wd.hWnd, GWL_STYLE);
	const DWORD exStyle = GetWindowLongPtr(wd.hWnd, GWL_EXSTYLE);
	AdjustWindowRectEx(&rc, style, false, exStyle);
	MoveWindow(wd.hWnd, rc.left, rc.top, rc.right - rc.left, rc.bottom - rc.top, TRUE);
	
	if (mouse_mode == MOUSE_MODE_CONFINED || mouse_mode == MOUSE_MODE_CONFINED_HIDDEN) {
		RECT rect;
		GetClientRect(wd.hWnd, &rect);
		ClientToScreen(wd.hWnd, (POINT *)&rect.left);
		ClientToScreen(wd.hWnd, (POINT *)&rect.right);
		ClipCursor(&rect);
	}
	wd.last_pos = p_position;
	_update_real_mouse_position(p_window);
}
void DisplayServerWindows::window_set_exclusive(WindowID p_window, bool p_exclusive) {