Just think Star Trek. There were all sorts of crazy things that they explain with sciences that don't exist. Who is to say that the creatures, beings, devices or anything in SFA cannot be science fictionally explained? You know what? I'll take a crack at it (I haven't played SFA in years so bear with me)
Staff: Exotic and strange weapons are no stranger to the Science Fiction genre. from what I remember about the staff it seems like some kind of matter alteration device. I can go into this more, but I will spare you some boredom.
Krazoa: Energy based beings have existed in many Science Fiction works in the past, a krazoa could easily be one.
Important crystals: it is possible to store vast amounts of data in a crystalline substance by marking it with very precise imperfections, and reading them with a proper mechanism.
Telepathy: it has been done so many times in science fiction, its no biggy
I probably missed something, but you get the point. besides, I seem to recall many science fiction elements in the gameplay. SFA is still within the science fiction genre, even if it has a fantasy action adventure feel.