Hmm, I'm by no means an expert on this thing but I'll hazard a guess! The auto throttle is controlled by a governor. Anytime you turn the switch from from AUTO to OFF and vice versa, there is a eletronic solenoid that moves the throttle. However, once the throttle is on a high rpm, the governor kicks in and maintains a steady rpm.
If the auto throttle is providing a too low of an idle rpm, I'd think that a simple idle adj using the idle speed screw (see my pic above) would suffice.
When I did the conversion from petrol to propane, I had to fiddle with this adj a little bit. Evidently the propane fuel requires a tad faster idle rpm than petrol fuel.
I don't know if I've helped any but there you go!
During my conversion project, I found this site Honda GENERATOR Parts Pre-1997 ES6500 A GENERATOR, JPN, VIN# GX360-1000001 TO GX360-1017635
to be quite helpful.