Hey Brewzer,
It IS possible to do step-ups and step-downs with the OOTB eccentric transition, however, just not when the height of both connections is the same. The formula the eccentric transitions use to modify how far they move up/down is: d = (|h1-h2|/2)*x (where | is the sign for absolute value). In this equation, the x is the Eccentricity Z value you set in the drop down list. For example, if your duct transitions from 20" to 12" tall, then setting x=1 will move the 12" connection up 4". If you wanted to move the connection up 8", you could set x=2, or for 6": x=1.5. However, if h1=h2, then h1-h2=0, and no matter what you set as x, you will always wind up with 0. It uses this same formula to calculate the eccentric offset in the X direction.
I've tried to create an eccentric transition that allows you to make step-ups/downs with the same size duct height, but I don't think I've had much luck. Part of the problem is that AMEP won't let you enter negative values except for in the Eccentric Offset fields that are automatically created when you set the part to be Eccentric. Unfortunately, there's not much control when using these auto fields. Maybe someone else out there has had more luck than I have.
I know this doesn't answer your question very well, but hopefully it at least helps clear things up when using eccentric transitions.
-Brad