"Ligatures in programming fonts—a misguided trend I was hoping would collapse under its own illogic."

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.

I certainly don't blame you for not noticing the `#fbf3f3` background color on hover. However, it seems that every link is either small caps or has that trailing ° character. It looks like the former is used for internal links, and the latter for external. I agree that they're certainly not screaming, but considering that the author considers this a book, that is probably by design.

then again, the signature is indistinguishable from small cap and isn't a link

In short it’s a design choice paying homage to some other books, as well as to make the reading experience less distracting. He has a whole page explaining here, https://practicaltypography.com/how-to-use.html

It's a pretty interesting approach to the website and there's some features I never would have discovered on my own, but the author's reasoning seems pretty poor. The premise being that multi-line stretches of underlined text are difficult to read, therefore link-text (typically 1-3 words) should not be underlined.

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

...and then he decided to put his name in small caps under the ligature article, and that one isn't a link.