As you can see, there's no stripe in the long shot. Nor is there one on Vader's shuttle on his approach:
"Ah," but you say, "Vader's shuttle isn't the Emperor's therefore no stripe!"
Then why are there two stripes on Vader's when he lands?!
First, sorry about all the pictures.
The stripes are the same in function (to the filmmakers and the audience) as the stripes on the X-wings. They are a design feature that was thought up to distinguish one shuttle from the other. Especially in the live shots where the actual shuttle set was used for at least three and maybe four different shuttles.
Palpatine's shuttle had one stripe perhaps to designate it as the Star Wars equivelent of Air Force One. Vader has two stripes and others don't have anyway. They were likely just stuck onto the prop and removed as needed. The nose of the shuttle prop also has a colored piece that was removed as well.
And then when filming began, the concept was scrapped. So the models and the sets don't match the matte paintings.
Note also the stripe on the nose of the shuttle that sort of matches the matte painting:
Here is Vader's shuttle with two stripes:
But it doesn't explain this which has one stripe:
And the Tyderium set-piece was repainted to make the shuttle the rebels were flying a bit more grungy and closer to the rebel's style.
So maybe the set designers, propmakers and painters had a plan for the stripes, but it doesn't show in the final product.