Laust: Notice that higher classes tend to run Lenco, Richmond, or Jerico 4-6 speed clutchless manuals. The reason that automatics take precedence over the T5/T56 transmissions is that the autos have planetary gear sets that have three contact points instead of one. They can take more torque. Richmond and Jerico transmissions are replacing Lencos in Pro Stock because of the weight difference. Planetary gear sets aren't light.
I seem to remember the phrase used in Hot Rod magazine during an interview: "If you're not using a Lenco, you're losing" (in reference to using a TH-400 w/ a clutch, as people have done in the past)
Automatics are faster in turbo diesel trucks because the torque converter allows the engine to stay in a higher power band (on the boost). And shifting 4-5 times on your way to 60 takes time. Why do people (like my dad) get manuals? They don't create as much heat when climbing with loads. And they can use the engine to control thier speed more effectively.
Turbo cars can easily have the manual be faster if the driver powershifts instead of lift throttle shifting.
Case in point:
Take the case of the 5.9 R/T Dakotas vs. the 4.7+5 speed. The quarter mile performance is so close, that it's always a good race and you never KNOW who is going to win. The 5.9 isn't available with a 5 speed because the 5 speed used (NV-3500) is rated for 300LB/ft. The 5.9 makes 260HP-350LB/ft. Clearly too much. The 4.7 makes 235HP-295LB/ft. Just under. So how does the 4.7 keep up with 25HP-55LB/ft of handicap? It lacks the loss of a torque converter and the drag of the automatic transmission. By the time it gets to the rear wheel, the 4.7s dyno at 204HP, and the 5.9s dyno at 207. A 31HP loss vs. 53. This is the primary reason why manuals are typically faster. Not shift speed.