Well, the CG shuttle in Empire SE is definitely different to the model used in Jedi and VERY different to the matte painting shuttles in Jedi. The main problem is that all the matte painting shuttles done for Jedi are completely inaccurate to the model, and the live action mockup used for some shots is even worse. So the Emperor's shuttle being different doesn't bother me, as it's only seen in one scene.

And yes, I did use the Empire SE shuttle, although I had to modify that too to make it somewhat more like the original model, as it also varies a lot. I've also added detail back onto the CG model that was on the matte painting shuttles.