If they are disguising, then why take off in a blinding flash of light and rocket to somewhere, kinda blows the cover. ;-)
I just watched a UFO Hunters where they highlighted tapes of two F-15 pilots reporting a UFO that looked like a huge rock that was gaining altitude, not falling.
I thought it was a brilliant disguise if extra-terrestrial.
Aviation lights do their work well if the observer has eyes that see in human range of wavelengths. It just isn't appealing to travel millions of miles and get into a fender-bender at the landing site.
If the UFO is indeed of extraterrestrial origin then it makes plenty of sense to modify the craft to conform to local aviation rules, if you don't want trouble.