### 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_
#if defined(VULKAN_ENABLED)
	if (context_vulkan) {
		context_vulkan->set_vsync_mode(p_window, p_vsync_mode);
	}
#endif
#if defined(GLES3_ENABLED)
	if (gl_manager) {
		gl_manager->set_use_vsync(p_window, p_vsync_mode != DisplayServer::VSYNC_DISABLED);
	}
#endif
}
DisplayServer::VSyncMode DisplayServerWindows::window_get_vsync_mode(WindowID p_window) const {
	_THREAD_SAFE_METHOD_
#if defined(VULKAN_ENABLED)
	if (context_vulkan) {
		return context_vulkan->get_vsync_mode(p_window);
	}
#endif
#if defined(GLES3_ENABLED)
	if (gl_manager) {
		return gl_manager->is_using_vsync(p_window) ? DisplayServer::VSYNC_ENABLED : DisplayServer::VSYNC_DISABLED;
	}
#endif
	return DisplayServer::VSYNC_ENABLED;
}
void DisplayServerWindows::set_context(Context p_context) {