Why did the B-29 have so much leftward torque at take-off?
It didn't arise ONLY during takeoff, but it is most noticeable then for several reasons


The engines are at maximum power, therefore producing maximum torque
You've got a very good reason to need to be travelling in an exactly straight line (the runway)
You're travelling at fairly slow speed, so your vertical stabilizer is less effective - at higher speeds, the tail counteracts the torque more effectively (for this B-29 this occurs at 80mph, as mentioned). As soon as you get above 80mph, you can just input a little right rudder to counteract it.... B-29's only travelled below 80mph on takeoff and landing, so it wasn't a problem during flight, and during landing the throttles were at idle or very low power.

It isn't true for all aircraft with more than one engine now (although it is true for some), but it does still happen and was much common back in WWII - they didn't want the extra supply line complexity of two different sets of otherwise identical engines, when it could be solved with a bootfull of right foot. Note also that the B-29 had 4 engines, most modern multi-props only have two, and they're closer to the fuselage, which reduces the effect
I think you're misinterpreting the source: he's not saying this technique was unique to the 509th, just that they were taught the technique. The very fact he says they were taught it, rather than "came up with" it, suggests it was known elsewhere. The 509th are only referenced here because that's the group Tibbets was part of, it's unrelated.