I'm kind of confused about this - I'm sure the author experiences real problems, but I wonder if there's something else at play here?

I've never actually seen screen aspect ratio media queries used in practice, nor have I really seen them advocated for. When I load www.theguardian.com on my portrait monitor (1441 x 2561) I get the desktop layout https://imgur.com/a/ZpUI95Z

Absolutely yes design your breakpoints around screen width. Using aspect ratio seems like a poor choice.