Torque Gain

[AudiA8Quattro]

Would the pistons not hit the valves though if you increased the stroke?

No because the pistons we used were shorter to allow the longer stoke, the block had to modified as well for clearance, was a awesome engine however so much torque.

A good example of this is the mk2 1.6 and 1.8 carb engines.
The block is the same for both engines. The crank and pistons are different to allow a longer stroke.
The bore is same for both.

[AudiA8Quattro]

that looses torque at the bottom end!

That depends on the cam choice, and headwork done.

I got a 25 BHP gain out of my head and cam set-up...with a gain it torque everywhere.

If you are careful about selecting cams and setting them up, you'll not always loose torque.

Doing the cams alone will lead to loss of bottom end torque.
However as you state, combined with head work this won't always be the case.