### 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.exclusive != p_exclusive) {
		wd.exclusive = p_exclusive;
		if (wd.transient_parent != INVALID_WINDOW_ID) {
			if (wd.exclusive) {
				WindowData &wd_parent = windows[wd.transient_parent];
				SetWindowLongPtr(wd.hWnd, GWLP_HWNDPARENT, (LONG_PTR)wd_parent.hWnd);
			} else {
				SetWindowLongPtr(wd.hWnd, GWLP_HWNDPARENT, (LONG_PTR) nullptr);
			}
		}
	}
}
void DisplayServerWindows::window_set_transient(WindowID p_window, WindowID p_parent) {