Does deeper axle gearing HELP or HURT the transmission?

i can't see much of a difference , the torque of the engine is the same no matter what gear is in it .

That's right, but the different gear can have an effect elsewhere. It's like using a 2 foot long ratchet in the place of a 6 inch long ratchet. YOU are still the same engine, but you can break the **** out of something with a 2 foot long ratchet.