I think that's overstating things a bit. They were working on real-time carriage rides in Skyrim, and nearly got them working (they had the carriage driver's dialogue recorded for pointing out places of interest on the way). A Bethesda employee released what they had as a mod, and modders got a passable implementation.
A 'proper' train wouldn't necessarily need clutter or companion AI either - depending on the implementation. If it was a bit like the vertibirds, and the player and companions just climbed on, activated it, and were then placed in their seats for the ride, then it wouldn't need much in the way of physics either (assuming we're talking about the metro system).
But that would, while straightforward and reliable, probably be dull. I assume you're thinking about an ambitious overland railway where characters can move around freely, it can be boarded by enemies, there can be fights from carriage to carriage... And I agree that could be challenging. But probably not as machine demanding as you're supposing, they'd just have to keep enemy numbers down. Bethesda's engine is surprisingly capable of handling rapid transit through the gameworld, and the AI load of lots on NPCs being (briefly) encountered.
The real question would be whether the feature would be fun enough to be worth the work. If it's just an A-B immersive travel... maybe. It was worth it for the vertibirds, after all . If not, then they'll have a very simple and restrictive implementation, for the sake of quick implementation and reliability.