Although transmissions don't make power they are a significant loss mechanism. So actually if you lower the trans loss (or improve its efficiency) you will improve power transmittal to the rear wheels.

All that said in general a manual transmission has slightly better efficiency than an automatic. For example look at the EPA mpg ratings for cars that come both ways. Why? Automatics have complicated planetary gear trains with more friction and hydraulic loss elements than manuals.

In terms of efficiency in automatics go the TH350 is relatively good. Powerglide is better and the TH400 has the highest loss factors.

The TH350 is a great fit for your application IMO.

Kitz