I'm not sure but I think an auto-trans ECU simply has more signals that go to the tranny. Those wires will just have nowhere to connect to. The sensors & signals for the engine may not be any different.

That leaves cleaning and proper adjustment of the idle-control stuff. If he's not real familiar with Hondas, he could have done the same thing with a car that has had a 5-spd from the factory.

Using one thing to compensate for another, is a shortcut technique with a long history. It takes time (& your $$$) to do it right. Many times it works OK, but you've discovered one situation where it DOES make a difference.