When I bought my 2003 Dodge pickup something like 60% of the diesels were sold with a manual, which is what I have even though I don't tow anything. I like the engine braking, putting along in a gear of my choosing, and most of all the robust simplicity.
A coworker didn't believe so many were sold with a stick, but agreed after buying one with an auto. A friend that also bought one also bought it with an auto, and both have been pleased with it when towing. While making small talk while waiting for a meeting to start people again didn't believe that so many were sold with a stick, or why I'd want one, but a couple of coworkers with Ford trucks piped up and said that they'd buy a manual the next time. The auto will be eaiser to handle, but on average a manual will last longer and have fewer problems. Some friends with autos don't expect it to last as long, and plan on rebuilding it stronger when it does fail.
Currently GM defuels their trucks in 1st and 5th gear in order to protect the Allison, and Ford may do the same per some descriptions that I've heard. One gentleman with an older Dodge that had a Cummins with a stick delivered a heavier than max load of hay to someone with a new Ford 6.0 diesel. The Ford owner couldn't even move the load, so the deliverer had to place the load for him. Automatics are about as complicated as engines, with a high part count, lots of wiring, sensors, actuators, etc., so you're about doubling the complexity in a modern vehicle. It won't be a big deal if you don't plan on keeping it long.