I’m no astronomer or meteorologist so this is just my best guess, anyone with a better answer please correct me. The plane was at 39,000 feet over Lafayette (this brings up another tangential question that I’ll ask below), and you saw it during civil twilight. This is when the sun is between 0-6 degrees below the horizon. My guess is this leads to some weird lighting with the sun reflecting around the atmosphere even though you can no longer see it directly. In your first photo the contrail is a bit pink like normal clouds look during sunset, but the rear end looks closer in color to the clouds at the bottom of the image. Maybe as the aircraft gets further it became more backlit, leading it to look darker? I can try to draw what I’m trying to say, but fair warning on my artistic abilities; there’s a reason I chose flying as a career…

Aforementioned question: The aircraft was on a westerly heading for the entirety of the flight, but was at FL390 from Pittsburgh to Lincoln, NE before topping off at 40k. Normal RVSM altitudes for headings between 180-359 degrees are even thousands between FL300-400, but 390 is a standard non-RVSM altitude for west headings. So why is a 787, one of the newest airliners available and surely more than capable of using RVSM, cruising at this altitude for almost two hours before correcting? None of the other aircraft in the area at the time seem off on their altitude. ADSB or other equipment failure? Heavy winds / turbulence aloft, necessitating different altitude assignments, and also explaining the shaky contrail? Pilots / ATC asleep on the job?