of Course what kills you when you fall is not the fall but the landing.but passing through the power core of a space craft seems likely to make your day even worse.. The issue I have with that theory is mostly the landing. also it's kinda soft for scifi.
My Theory) "The Dark Daniel Jackson"
Vader tossed the old fart off the Bridge,
the Emperor is falling see's his death is coming he or some other darker power Uses the Force to transmute his body and teleport or ascend into some other nonphysical form and then at a later date and time he reformed on this junk planet.
(This is basically What Doctor Jackson did in Stargate SG1 when he was dying.) A hint of this is in Starwars Episode 3.
"Darth Plagueis was a Dark Lord of the Sith so powerful and so wise, he could use the Force to influence the midi-chlorians to create life. He had such a knowledge of the dark side, he could even keep the ones he cared about from dying."
So the Emperor Emerges but in the process he is mutilated and so he uses the machines to rebuild him self.
Theory 2) Max Von Sydow is not the emperor but Boba Fett left for dead inside the beast his mind and body broken he found away free. And the new evil will take another form.
And If Palatine is still involved perhaps a Ethereal form emperor will posses or take under his influence a new student to once more build the Sith order much like how Obi Wan still taught Luke after his death.