You and I are the same size at 6'1" and being long legged. The good news is the Pilot has a long steerer tube relative to top tube length so you will still get a good measure of handlebar height compared to how stretched out you are with your proportionately std. size torso. In effect that bike will ride for you more like a bigger std frame Trek 5000 except it will have a bit shorter reach...not a bad thing for your proportion. If I were buying a Trek Pilot, I may very well choose the same frame size and I prefer a big bike...I ride a 61cm c-t-t mildly sloped top tube Bianchi. With your torso length you would likely feel too stretched out on a 63cm Pilot.
Hope that gives you some peace of mind.
George