Hi Dan, Plasma version has touch off in the program to set the Z zero and is nearly impossible to set heights for routing.
What Masso can do is supply both Mill and plasma programs and you can use two usb sticks to hold your settings for each.
We all have had the same thoughts as you do but found it isn't viable having both on the same table unless you have a very long Y axis.
Say front Half for routing and back half for plasma.
I have heard some one is doing two tables, one for each and will unplug the cables from one to the other and reload the program to suit. Very quick and easy to do when you think about it.
Hope this helped a bit,
Ross