I'm a Face of Boe girl myself. I figure, over millions and millions of years all sorts of things can happen. While Jack can't die, it doesn't mean that he can't physically change. Possibly it's an effect of the Time Vortex stuff. Perhaps as he gets older and older the Time Vortex starts to wear off, it starts doing weird things to his body... or else he becomes a giant head for the sake of life support or something. I know, I know, you'd think that by the time he needed life support Jack would be ready to die, but wasn't Boe on life support in Gridlock?

Oh God--it just occurred to me that if Jack doesn't die eventually, he'll probably end up as a Toclafane. Brrr.

... and is stumped. A humanoid cannot become a tentacled head in a jar. Well, not with science as it is now. I mean, you could cut the head off a humanoid and *put* it in a jar, but that doesn't explain the tentacles. Does this head, y'know, live? Or is it a preserved specimen?

As to the sex-change, well, those happen. I don't know the canon or the details though, so I can't comment any further.

*Biology goes away to change out of the ridiculously uncomfortable spandex*