That's definitely one part of it: thumb-scrunching-to-cmd requires less wrist movement, for me at least, than ctrl+[anything]. Re-mapping caps lock as an extra ctrl helps a ton, but cmd is a much better default than the ordinary ctrl, for very common system-wide keyboard shortcuts.

In fact, I just checked out of curiosity, and I move 2 fingers very slightly to cmd+c, while doing (standard) ctrl+c I move every joint up my arm, including my shoulder, and all my fingers (as I reposition my whole hand, so the fingers all flex, flattening so my pinky can hit the ctrl)

Again, caps-as-control makes it much better, but I can still feel more strain than the very natural almost-pinching motion of cmd+c. I don't know how much of this was intentional when the Apple keyboard was designed and shortcuts chosen, but it's a real effect regardless.