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. He hid himself in plain sight and donned the black plain robes once he had secured the Galaxy for himself.
But - if Ady like the idea of making something new and special for Emp - I’m not opposed, but do not see the necessity for it.