My suggestion: make the Emperor’s shuttle unique, paint it red, or black, with the Imperial logo on the side or something.
Why would the Emperor paint a target on himself? Palatine is not as vain and ego-centric as Krennic or others are.
Well it’s not like he would travel alone without a Superstardestroyer and some “small” stardestroyers.
Good luck getting near that shuttle.
Im sure if he doesn’t want attention and goes alone, he won’t use that.
I far as I know, there is no one more ego-centric in the whole star wars universe than the Sith.