I always hated the theory that T-Corp is deliberately inducing the bajillion year stasis because it blatantly ignores the horror of The Jaunt by making the suffering optional instead of a requirement. I like the explanation provided in Dante's notes though, the train is literally running on human perception of time in order to travel through the warp laterally through time itself. The box is just there to siphon it to the "engine", I think. That makes it extra fucked probably.