The article is following the predominant formatting method for Lisp dialects. What you propose is not unheard of, even in professional code bases, but very rare.
In the predominant style, nobody worries about which specific closing parenthesis goes with which opening one. The indentation reveals the subordination structure, and the editor takes care of that.
Speaking of indentation, you have it wrong: the sqrt should be indented inside the let.
(lambda (x y)
(let ((xs (* x x))
(ys (* y y)))
(sqrt (+ xs ys))))
^^^^
At the ^^^^ spot, all that matters is that we have four closing parentheses. They are all the same otherwise. Which specific one closes the let is not informative.
There are too many parentheses to be focused on them; you have to learn mostly not to see them, except within a line of code where there is no indentation. Someone who has been working with the language for a while just "sees" this:
lambda (x y)
let (xs (* x x))
(ys (* y y))
sqrt (+ xs ys)
Or maybe even this:
lambda (x y)
let xs (* x x)
ys (* y y)
sqrt (+ xs ys)
(The question of "why not make
that the syntax" has been thoroughly explored; it exists out there in some forms, along with other proposals for alternative Lisp syntaxes.
https://srfi.schemers.org/srfi-110/srfi-110.html )