### 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
windows[MAIN_WINDOW_ID].wtctx = 0;
		}
		DestroyWindow(windows[MAIN_WINDOW_ID].hWnd);
	}
#if defined(VULKAN_ENABLED)
	if (rendering_device_vulkan) {
		rendering_device_vulkan->finalize();
		memdelete(rendering_device_vulkan);
		rendering_device_vulkan = nullptr;
	}
	if (context_vulkan) {
		memdelete(context_vulkan);
		context_vulkan = nullptr;
	}
#endif
	if (restore_mouse_trails > 1) {
		SystemParametersInfoA(SPI_SETMOUSETRAILS, restore_mouse_trails, 0, 0);
	}
#ifdef GLES3_ENABLED
	if (gl_manager) {
		memdelete(gl_manager);
		gl_manager = nullptr;
	}
#endif
	if (tts) {
		memdelete(tts);
	}
	CoUninitialize();
}