No, whether I put the controller back in the circuit or not I get the same result now. The car cranks but does not turn over. Seems like it’s doing what this honda bulletin discusses on page 2: http://www.hondalac.com/service/Bulletins/x01-053e.pdf
“If you try to start the engine with a nonprogrammed ignition key, the engine cranks, but it cannot start.”
Except I don’t know how me messing with this aftermarket anti-theft system is affecting the stock Immobilizer System.