This is no concept of "app" in GBW but there are additional files you can add to your image and put them in to any folder you like.
And NO, please dont use any WAIK or other tools on WIM files supplied with GSS. We craft those WIMs such that we can inject drivers and files numerous times. We can guide you as to how to fix them but in general if you use any 3rd party tools and broke GSS files you'll be on your own :( Files are bootable (as you probably know from any media that we support and you tried on) but they are of a slightly more complicated structure than your regular simple WIM.
Hope this helps.