Now if that were 100%, wouldn't people that use a manual switch to lock their trans in second gear experience breakage when they shift to 3rd? If you have a light hooked up, by the time you react and flick the switch to lock the TCC, the trans should already be fully in third gear.
Realisticly, racing a car is hard on the transmission, period. You can do whatever you want to go faster, but as you do go faster, you are placing more and more stress on all the drivetrain parts...not just the stock input shaft.
FWIW, the only two input shafts I ever saw break, broke at the starting line as the car launched. Joe Reif can tell you of his experience.
My daily driver (back when I used to race it) ran 12.70s with short times faster than 1.65 on slicks and never broke a thing in the Mike Kurtz built tranny. The transmission in my fast car ran with a stock input shaft for years and never broke (The 1.51 short time was with the stock shaft). I did have Lonnie put a fancy input shaft in for this year as I had every intention of flogging the car in TSM. 
