I'm not familiar with the limitations of the system, and I know the point is speed, but couldn't they just slow down before traversing the obstacle?
That's a delta-v of at least 700km/h or about 200m/s. At a deceleration of 1g it'll take about 20 seconds, and an other 20 seconds to get back to speed after that. And 1g sounds like a lot for public transportation, especially for so long. Maybe they could rotate the seats to keep the acceleration downwards from the point of view of the passengers?
And obviously it'll take a lot of energy to re-accelerate the car, so you might want to store the braking energy to reuse it but I'm not sure if it's practical to store such a huge amount of energy so quickly.