I think manual transmissions vs auto transmissions are personal preference and whatever one has available but I have found a few advantages of the auto transmissions.
My first gasified truck was a 78 F-350 ford with a manual transmission but all afterwards have been automatic.
On the road I would see no difference in transmissions but in tight parking areas and farm work, hooking to trailers ect. I find it is so easy to hold a little throttle and let the auto trans and the torque converter do their job.
Sudden accelerations and decelerations will cause the inertia of the gas stream to momentarily throw the air/fuel ratio out of the correct mix. ( going from throttle to brake )
I have noticed if the gasifier is not up to good operating temperatures and waiting to pull out into traffic one can hold some throttle and the brake. When you start out in the traffic letting off the brake will start the vehicle with no more load being asked of the gasifier.
I am sure one can teach himself to overcome any of the above problems.