It's not about "difficulty" ... as in one takes 5 calories to type out "that's stupid" but the polite sentence takes the same effort or less.
It's about effectiveness and possibly the false cause & effect we attach to one style of communication vs another. E.g. Linux may be successful because Linus is direct and blunt. (It keeps idiots wasting everyone's time away.) Or, Linux is not reaching its full potential because Linus is crude. (It drives talented contributors who are repulsed by crude language away.) We don't know which scenario is superior because we can't replay history in 2 separate universes.
To your particular example, I personally don't like the "I'm confused by this." That is what I call unnecessary "prelude". It's redundant prelude because Allen's next paragraph clearly asks 2 questions so of course he's confused.
Also, Allen writes:
"Can you take a step back and explain your goal here?"
Again, my personality doesn't require business language ceremony of "can you take a step back..."Allen can delete "I'm confused" and "take step back" and get directly to the point:
"Can you explain your goal here?"
However, I want to emphasize that even though I don't like ceremonial language ("polite" as some may call it), I accept that some people require prelude & ceremony so I do write many of my emails similar to Allen's style.