Why not have seats on the pod, that way you don't have to ferry around a 2-tonne car. Indeed if you have solved smart automation, why have rails at all? Presto, you arrive at the idea of self-driving taxis as a public service.
Really, the car would (should!) still be driving itself—it's the thing that gets certified on how to handle safety issues, after all; the car would just be given a dead-reckoning location target by the zone controller, which the car would get to as best it knows how, with the zone controller scanning to "see" when it had successfully boarded, just like with a human-driven car.
If there were few-enough human-driven cars, you could have a team of valet staff accompanying the train, acting as glue for the few human-driven cars in the pack.
That wouldn't remove the need for ventilation and other things you mentioned if that system is underground. But it could be above the ground , on buildings 2nd floors, where the first floor would be retail stores and whatnot