Had a Banks turbo on my 2006 LJ auto for 3+ years with no trans problems. The 42rle is a computer controlled transmission and the computer limits the torque to trans to a safe level. Shouldn't be a problem.
I am glad it doesn’t limit my torque too much. It goes pretty good when you put your right foot in it. I was almost able to keep up with a Camry on a steel hill yesterday. That says something for a TJ.