I just thought of this theory. It's definitely possible that I'm not the first one, but I don't remember anyone ever mentioning it and the wiki doesn't have this either.
So, QB can be seen by the megucas, but not by other people. Doesn't that seem weird? Sure, he is an alien and has evidently access to very advanced technology, but what kind of technology makes him invisible and not invisible at the same time? It doesn't make any sense. Furthermore, in episode 02, he is seen taking a hot bath in the presence of both Madoka and her mom. We see what it looks like from Madoka's point of view, but if there really was an invisible QB in the water, it would look incredibly retarded from Junko's point of view, but Junko doesn't notice anything.
Also, his telepathic abilities confirm that he is capable of "invading" the minds of people at least to some extent. Therefore, I think that it's reasonable to assume that what we see is not QB's body, it's an illusion of sorts; he uses his mental skills to make people see him even though he actually isn't there. This would also explain how he can have unlimited bodies.
The problem with this theory is that if QB isn't physically there, then how can he make the Soul Gems and dispose of Grief Seeds?