You should be running a slaved axis. Let Mach send step and dirextion signals to the A axis on the BOB and connect your A axis drive to the A axis on the BOB. You already have the parts to do it. You just need to rewire a little and set up the A axis in Mach.
What he's done should work just fine. AFAIK, the only thing he's lost by NOT setting it up in Mach as a slaved axis is the ability to "zero" the slaved axis through the GUI.