Hmm, pitashen, while I see your point, I think what would make tkl more ergonomic is that, if you are right handed, at least, the mouse would be closer to your home rows, so you wouldn't need to move so much to reach it every time. Since you may be reaching for your mouse very often, that could contribute to your rsi, at least in the severity of the stress, rather than the number of repetitions.
That being said, I was getting wrist pains in my right forearm, and I decided to start using my mouse with my left hand, and I've learned to use the mouse less and less. I think habits end up making a much bigger difference than the gear you're using, so if you have RSI, or think you are developing RSI, I think adjusting habits is more important than buying new things (as I'm sure other people will tell you if you ask).
Stay strong! RSI is a bugger