The article is about keyboards used for programming and not ergonomics per se. I've been programming for some 30 years, 15 of those on a Kinesis and more recently on a TECK. Before that was standard PC keyboard layouts which are the worst.
The most important thing to a programmer is easy access to all the keys you need, which is every key on the keyboard since we use all the odd ones frequently. The navigation keys are probably the most important as you spend most of your time scrolling around and putting the insertion point somewhere. Both the Kinesis and TECK get high marks in this regards as they both prominently configure those keys in different ways. I prefer the dual symmetric arrow blocks of the TECK, but the Kinesis nicely puts those right below the home row so a hand shift isn't required.
Secondly you want good and easy access to the modifiers and accessory keys like Return, Space, Tab, Delete and Backspace. You use all of those keys a lot! I love how the TECK has dual symmetric modifier keys (Shift, Command, Meta and Control) on either side, with the rest of them all in the center. The Kinesis has them scattered around with not a full dual set of symmetric modifiers, and no Del key I believe or one not easily accessible (on an eraser). Speaking of which full mechanical Function keys! The Kinesis has them all on crummy eraser keys.
As for the letters they should just be QWERTY for muscle memory. You just type variable names and reserved names so those can be written just fine in QWERTY.
