This was not a regular marathon course, it was EXTREMELY hilly. If you don't train every week multiple times on hills, you are at a massive disadvantage, also if you have the wrong body type for hills (being tall, like 185+ for men or 170+ for women, not the case for mentioned runners tho).
Molly Seidel posted her whole training log on Strava - she acquired a significant amount of elevation during the last 12 months. I run on hills and mountains every day, and she only has 10-20% less elevation gain per mile than I have - which shows that her training was always in hilly areas, and especially once she got notified about Atlanta's course she did even more hills.
She also did a lot of hill sprints in workouts each week. Her training is similar to Tinman/Lydiard - lots of mileage, lots of hill running, hill sprints, no hard intervals, a lot of work around threshold and strong tempos/long runs.
The Kenyan-born runners obviously are also used to train on hills, especially the one who still trains in Kenya.
Would Seidel have made the team on a flat course? Likely no, but that's the beauty of marathon running - you can't predict the outcome like in a track race, were conditions are always the same and the outcome is much more predictable. Was it smart to run a hilly marathon when the Olympic one will be totally different? Probably not, but it doesn't really matter, no one expects a US runner to get top 3 in Olympics anyway.