### 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
}
#endif
	mouse_monitor = SetWindowsHookEx(WH_MOUSE, ::MouseProc, nullptr, GetCurrentThreadId());
	Point2i window_position;
	if (p_position != nullptr) {
		window_position = *p_position;
	} else {
		if (p_screen == SCREEN_OF_MAIN_WINDOW) {
			p_screen = SCREEN_PRIMARY;
		}
		window_position = screen_get_position(p_screen) + (screen_get_size(p_screen) - p_resolution) / 2;
	}
	WindowID main_window = _create_window(p_mode, p_vsync_mode, 0, Rect2i(window_position, p_resolution));
	ERR_FAIL_COND_MSG(main_window == INVALID_WINDOW_ID, "Failed to create main window.");
	joypad = new JoypadWindows(&windows[MAIN_WINDOW_ID].hWnd);
	for (int i = 0; i < WINDOW_FLAG_MAX; i++) {
		if (p_flags & (1 << i)) {
			window_set_flag(WindowFlags(i), true, main_window);
		}
	}
	show_window(MAIN_WINDOW_ID);
#if defined(VULKAN_ENABLED)
	if (rendering_driver == "vulkan") {
		rendering_device_vulkan = memnew(RenderingDeviceVulkan);
		rendering_device_vulkan->initialize(context_vulkan);
		RendererCompositorRD::make_current();
	}
#endif
	if (!Engine::get_singleton()->is_editor_hint() && !OS::get_singleton()->is_in_low_processor_usage_mode()) {