The counter has a capture, good to the microsecond. Triggering basic motion behaviors can be done in AXSCRIPT. Neither gives you the ability to move the axis relative to something else. You could do it, but it would involve some math gymnastics.
I am thinking back to two applications I have physically seen, both involved moving an axis relative to an encoder input. One was a simple flying shear, cutting plate glass as the glass was moving down the line in one continuous ribbon. The other was a machine that made steel studs, where the material rolled into the machine at a constant rate, while a moving punch would move to three positions on the stud and punch the conduit routing holes, and then a shear would cut the stud off. In both of those cases you have material moving at a constant rate, and a moving tool that needed to match speed at one or more positions. That would be a booger to do without some specific abilities in the hardware.
So, I'm now thinking about some kind axis to encoder relative move, where you could tell the axis to sync with the encoder at a position relative to the registration mark. It would move to the mark relative spot and then track it. You could trigger other actions while registered, then move to the next mark relative spot and do more work. For the glass shear, you register, sync at the offset, then run the shear while tracking. For the stud puncher, you register, sync at offset, punch, sync at second offset, punch, sync at third offset, punch, then run back to home and wait for the next registration mark. Even Bernie's slaving one axis to another would naturally fall out of such a feature.
Does that sound useful? If so, I could see it as a function for AXSCRIPT as well as a standalone box.