When I check someones your code and edit it, I get plain text - no ligatures, fonts, highlighting, themes, etc are included. I don't know what dev setup forces visual choices on coders, but that sounds like bad idea...
Here he's referring to code in books, slide decks, and during presentations, not for editing.
Just below the section the above quote is pulled from, Butterick explains
> One inspiration for this piece was the LaTeX crowd, who would routinely write me to insist their typography was infallible. And yet. I kept seeing LaTeX-prepared books that incorrectly substituted curly quotes for backticks.... “But code samples like these aren’t really ambiguous, because everyone knows that you don’t type the curly quotes.” ... But many of today’s programming languages (e.g., Racket) accept UTF-8 input.... So ambiguity is a real possibility. Same problem with ligatures.