I really though Bill was going to be in that episode too, but my next theory is that the "Apocalypse" Isn't over yet. That it's just starting, and the portal itself isn't going to do it. If you look behind Stan's brother into the portal. It's all grey, like the dreamscape. I'm thinkin something weird is going on. As well as this
Oh, well maybe it could be because he's been searching to help his bro for a long long time and he's always been on his mind hence why it's in his mindscape. The new image could possibly tie it all up, saying why it was there. Perhaps that place/moment was extremely important to him.
Alex Hirsch said something about that being why Stan was so upset when wax Stan got "murdered" it's because he missed his brother and was never really able to give him a proper good-bye. So he used the wax Stan as a replacement for him.
Well I do love a lot of epps. Double Dipper, Bottomless Pit, Dreamscapers, Into the Bunker, ((I'm a fan of the Thing.)), Sock Opera, and Not What He Seems. You?