It turns out you can NOT do what I had proposed... hardwire a controller directly to the PowerRise headrail, nor can you combine headrails on one IR receiver.
The reason has to do with the way the IR eye is connected and what it does. For reasons having to do with power savings (default is that unit is battery powered), the pins do multiple things... the processor pin checks the state of the IR receiver but also switches to an output pin when the processor is sleeping (not checking IR status)... so wiring headrails together creates a ground loop without additional circuitry.
You can't connect the units directly to a controller either as the IR eye is sending demodulated data to the headrails, not simple up/down requests or modulated IR codes.
So the best solution for now is to tie standard IR emitters directly to the IR receivers... but I'm hopeful Hunter Douglas is hearing these requests and considers coming out with an interface to help us automators...