I agree as well with the point about ligatures, but I find funny that the advice comes from a site that thinks straight up normal text with no hover, no distinct color, no distinct font and no underline is a good way to signal linked pages https://i.imgur.com/9iVMfgD.png (who would have guessed Racket was a link?)
The same could be said about so many programming conventions most people take for granted. Sometimes programmers are their own worst enemies. "just because you can doesn't mean you should" is probably the #1 rule of programming, at least for me, and ligatures definitely fit into that category.
It's also quite ironic that the author's argument against ligatures in programming fonts is that the simple substitution doesn't respect semantic difference, whilst using emphasis to signify that there is a link present