Here's a question, I know why it can't happen for setting reasons. However, they put basically dead space marines into juggernauts, but why not the emperor?
Also, why isn't he healing? He's human, they have fairly advanced healing methods. Why isn't the emperor able to heal? Obviously ignoring the Gilligan Paradox. (i.e. 40K would be over because the emperor basically insures victory for Mankind.)
Right off the bat we can assume that putting the Emperor in a Dreadnought would be some kind of sacrilege or another. Moreover, I believe the general perception in the Imperium (of those who actually know that the Emperor is on the Golden Throne) is that he wants to be there. It was his last proper command to entomb him upon it, wasn't it?
Also, interment into a Dreadnought is sort of . . . well it's honorable to be sure, but it's also kind of a second death sentence, since once your Dreadnought is destroyed that's it, end of game, there's no coming back. You can imagine why no one would be willing to risk that. There might be more sense if you had like a Titan sized Dreadnought for the Emperor however. In fact, let's just assume that if shit ever really hit the fan again, the Emperor's Palace on Terra can transform into the biggest, baddest, most grimdark megazord ever.
Also, he doesn't heal because the Golden Throne prevents it. In the same way that patients on life support sometimes become dependent upon it, the Emperor won't heal because the Golden Throne was designed to truly immortalize the Emperor, up to and including preventing him from healing to move beyond it.