Oh I'm all for varying the shuttles, I just don't agree with the reasoning necessarily. I think it's pretty clear that Piett does know something once Vader has joined him, you can see it in the look he gives.
Anyway, I was also swayed by the fact that it will be a hell of a lot easier to alter the Emperor's shuttle than Vader's or the Rebels.
As for why the Rebels do have the same design, well I prefer non-universe explanations for things like that; those being that the movie was made on a reasonably tight budget and it was easier to do that with the time and money they had.