### 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_V(!windows.has(p_window), WINDOW_MODE_WINDOWED);
	const WindowData &wd = windows[p_window];
	if (wd.fullscreen) {
		if (wd.multiwindow_fs) {
			return WINDOW_MODE_FULLSCREEN;
		} else {
			return WINDOW_MODE_EXCLUSIVE_FULLSCREEN;
		}
	} else if (wd.minimized) {
		return WINDOW_MODE_MINIMIZED;
	} else if (wd.maximized) {
		return WINDOW_MODE_MAXIMIZED;
	} else {
		return WINDOW_MODE_WINDOWED;
	}
}
bool DisplayServerWindows::window_is_maximize_allowed(WindowID p_window) const {
	_THREAD_SAFE_METHOD_
	ERR_FAIL_COND_V(!windows.has(p_window), false);
	
	return true;
}
void DisplayServerWindows::window_set_flag(WindowFlags p_flag, bool p_enabled, WindowID p_window) {