So picture parallel tracks with a merge-point somewhere ahead (or a few, in case one doesn't work). You've gotta split the train, merge in the new car, and merge it all back together, at moderately high speeds. Not much of a fun engineering challenge, methinks. The top-car probably makes more sense in this case. At low speeds, where all cars can be the same shape, certainly. Just remove / add to the front / end as needed.
My favorite design of PRT was always SkyTran, featured in a Popular Science or Popular Mechanics magazine years ago: http://www.skytran.net/phpsite/home/Home%20Intro.php
Real world engineering issues aside, my gut feeling was that a suspended/hanging pod would offer more stability and ability to accelerate than a traditional pod resting on top of tracks. If the pod could swing back and forth, acceleration and deceleration would push riders down into their seats rather than back or forward toward the windshield.
The Big Bad Wolf and Batman roller coasters come to mind. :)
Each "car" holds just 2-4 people. they run on the tracks and switch on and off at the right stops. Very granular.
But still like a train in that you have tracks and power from the tracks. There is no conductor then, so everything would have to be computer controlled.