Daryl, This car looks to be not from the latest runs, shows 2012 v2 catalog. From the MTH website it shows the Kadee Mounting Pads, doesn't look like it has all the details of the later runs.
In terms of your other questions
Do Atlas 2 rail trucks always come with the MTH 3 rail plugs conversion in the packaging or do you have to request them? Always in the box.
Do these same plugs allow you to convert Atlas 3 rail cars to 2 rail cars? Inserts not necessary for converting Atlas 3R cars.