> ... if you’re prepar­ing your code for oth­ers to read—whether on screen or on pa­per—skip the lig­a­tures.

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.