Well, first of all, like the man said, "We don't have a choice for the SRT-4." Second, if we did, I wouldn't want the Neon auto trans anyway since it's not strong enough. Don't know about the one in the PT right now.
Which trans is best depends on what you are doing with the car. You wouldn't want to try to auto-x with an auto trans. An auto with a manual valve body is lots of fun on the street (I know!) and is even better at the drag strip. In the 1/4 a properly set up auto will beat a manual every time, all else being equal.
If the SRT was offered with an auto trans that I knew could handle the torque I would order it that way. Have you ever driven a car with a properly set up auto trans?