An interesting discussion for sure! It sounds like both the manual and auto choices for the HDJ81 are reliable enough (when maintained), sounds like a toss up more based on preference and availability. I'm not a Landcruiser guy per se, but I would assume we're talking about the H150/H151 (For the manual) and the A442F for the auto? Both seem to be great transmissions.
I'm a manual transmission enthusiast myself and the vehicle I'm building up has one of the more robust overdrive manual transmissions that has ever been offered in a vehicle in north America. With that said, even though I love this particular transmission and some of the advantages it has in gearing for certain situations, if I were to build a specific rig for overland travel, I'd pick an auto every time. Ease of use, especially in stop and go traffic or over rough terrain would be the big reason. Modulating everything while navigating complicated areas or obstacles gets a little old with a manual after awhile: heel-toe sidestepping of the brake and throttle and a long-throw, high-effort clutch pedal makes what would be relatively simple task in a automatic rig a lot more work with a stick. Driver fatigue can and often does go up. Mechanical fatigue in the drivetrain also appears to be greater in a manual transmission rig. Shock loads _seem_ to be a little better managed with a automatic (torque converter) and a thoughtful pilot. Just my humble opinion.
I've had a clutch failure in a manual transmission and torque converter failure/pump failure in an automatic rig. Both were still able to limp to a safe spot to get checked out, although it was painful in both vehicles. Given an opportunity and the right situation, everything can and will fail. The key is have a good idea of what you'll do to handle it if and when it does.
I would would put an emphasis on making sure whatever you choose starts out healthy, stays healthy and has proper upgrades to maintain that if required and then just go for it... If both transmissions were 100% reliable, what would you choose
@SoyBoy?