Heres my feeling on this, I'm no pro puller but have put a lot of thought in to this myself.
All the points you raise about autos are valid, and to some extent make sense. But there is a point about the manual that still puts the advantage in its hands in my opinion. Best I can explain is this. Suppose you are leaving the line with the auto, lets assume your motor turns 4,000 rpm. You come up on the converter while on the brakes and start building boost, depending on your stall, lets say your convertor starts locking up around 2500 rpm at which point you release the brakes and start the sled moving. At that point, the power of your motor needs to be able to overcome what drag the sled is putting on it to achieve maximum rpms. And many guys have enough power to do so. Some don't, and they will never see maximum rpm. As autos get stonger and better and the builders get more creative, they continue to find ways to make them work better. But no matter what, the fact remains that with a manual and the right clutch, the truck can establish, and maintain, maxumum rpms, wheel speed and power with the ability to "feed in" the drive to the wheels. Assume the same motor as the auto scenario only with a manual. Now you bring rpms up to redline - 4000 rpm, and slowy start feeding some clutch out, as boost builds to peak levels, clutch continues feeding out, wheels start turning, all the while rpms never fall below 4000 - assuming proper gear was chosen and all else is well. Not to mention, the really big power trucks can spool those HUGE turbos better with the manual because they can establish very high rpms before ever loading them at lower rpms the way a auto has to.
It is a strange concept that I don't fully understand myself, but it obviously works as the strongest trucks in the country run clutches. Not to metion, sled pulling with an auto and shifting with that kind of load is hard on any transmission no matter how it is built.
Someone who knows more will likely put me in my place - but there you have it.
As for manuals spinning the wheels more initially. That is likely. As I mentioned, they are leaving the line full tilt, and one can only be so smooth getting the clutch out with the motor at redline. Besides, if the wheels are spinning, less chance of things breaking.
Anyway, as I said I'm no pro. But this is how I have come to understand it after spending quite a bit of time thinking about it. But there are lots of guys who do pretty well with the autos, have to wait and see whats next.