Most of stress injury derives from the "time under tension" component which is not necessarily a matter of key travel distance. In this case it's a combination of switch mechanism and keycaps. Flat and light keycaps have less force at rest than tall, heavy keycaps. A higher resting force means the needed activation force is lower. In both cases, the switch is governing how much force is needed in total, and whether there's a "tactile bump" indicating activation before the switch bottoms out completely.

When the switch bottoms out, it's like your fingers have hit a wall: this is the norm with most membrane switch designs, and with linear mechanical switches, which are usually light. With tactile and clicky switches, the concept is to reduce bottoming out by indicating the activation with heavier force partway through the downstroke. A pairing of heavy keycaps and heavy tactile switches is often considered satisfying for typists because then the heft of the switch has been balanced out; a light tap will fling the key down past the tactile bump and spring it up without the same degree of muscle activation as a linear switch. And it is possible to have "too heavy" keycaps for the switch, which simply won't work(always activated).

With the key height, as well, what will matter is tension at rest, which will depend on overall posture. In theory you move the keyboard down if the keys are taller.