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
