Its a design for comfort/optimization.
A desk usually runs parallel to our arms, but our fingers are usually still spread horizontally. So the keys are arranged so that the keys furthest away are where the finger is most stretched out and the lower keys for when you're pressing down at more of an angle. Basically to reduce the need for us to bend our fingers at a near right angle. Even if you "don't use the home row" your hands are usually going to be in the middle of the keyboard. Obviously its not that different to a flat key setup but its more a subtle optimised design.
Also the distance thing does make sense. You're calculating the distance, but you didn't take into account that people have fingers. If its a flat keyboard and you're trying to press 2 keys at the same time, if you're all the way stretched out you arch your finger and thats where you lose the distance. Where as on a stair thats less of a problem because its slightly raised up to you and the levels are seperated?
I hope people understood that, its kind of hard to demonstrate without pictures, but it makes sense, because of lots of little things im not even going to bother explaining because Im yapping on here lol