My manual transmissions are both diesels. The one on the right has the added second security stick in it.
The 2003 Beetle TDI is manual because the automatic transmission of that era is simply trash. If you want the bulletproof VE engine you get a manual.
How many $2500 auto rebuilds is your tolerance with the Cummins powered truck. If they were sold with Allison automatics i would feel differently, but the doge transmissions had a plethora of failure paths. 600 ft/lbs of torque @ 1600RPM tends to find them.