That's actually surprising to me . . . I wouldn't have guessed the shorter "southern" route had more elevation change than Sandy's route. When I think of states like California (especially southern CA), Arizona, Kansas, Missouri, Indiana, etc, I think of pretty flat states.
Also, keep in mind, even on a seemingly flat road, 5000 ft of elevation change over the course of a day is not uncommon. Every road has dozens of feet of minor undulations per mile, even ones you would swear are pancake-flat. For example, my Daytona 100 Ultramarathon has something like 4000 feet of elevation change, even though you cannot spot a single hill on the course (except for one bridge).
At any rate, Sandy didn't do some side-by-side comparison of the two routes and decide the longer northern route was easier, and therefore pick that one. (Actually, the opposite is true . . . she wanted to follow in the footsteps of Marshall and Pete and take the route generally-recognized as the more-difficult one).