There is little evidence the QWERTY itself is the cause of RSI or Carpal Tunnel. However it is considered as a contributing factor; that and the design of the standard keyboard layout. The position of the hand and the wrists are really not ideal.
If you're looking for a direct link in such a complex behavior, which is—to make things worse—insufficiently studied in detail, you're in for a disappointment.
There are clear-cut arguments to be made, though. If a combination of a typing technique and a layout reduces, say, same-finger ratio, such repetition is reduced. Ditto if the layout helps reduce typing errors (i.e., there are fewer corrections needed). If the layout makes learning to (touch) type easier, users are more likely to use such technique and gain respective benefits (such as lack of eye/neck strain from checking the keyboard while typing).
However many typists live with it and have no issues at all. I have a friend who is amazingly fast on QWERTY. You literally like hear 5 keystrokes and when you look at the screen, there's quite a long sentence with punctuation.
So what. I can run 5 km faster than 99.9% of people, and that's without training. The smoker across the street has lived to 90. And so on.
It is a proven fact that Dvorak does alleviate the pain of those suffering with RSI and Carpal Tunnel.
Really? I'd like a citation on that.
The question is which of the two has more of an impact in reducing the risks.
And as I've said, those are two different things and it depends on circumstances.
If only use hotkeys most of the time and don't type, I'm not getting any benefits from a layout optimized for typing; in fact, it might be getting in the way, if the key bindings were designed for another layout (US QWERTY).
If I needed to type, but couldn't touch type, using a keyboard like Kinesis Advantage would be counterproductive by making the "hunting" part of "hunt and peck" more difficult. However, a suitable layout might help me learn to touch type.
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