The fact that file extensions and TLD's were roughly the same length in the same format wasn't a big issue, when it's generally understood that ".com" and ".edu" are domains, while ".jpg" and ".mp4" are files. (And as the author states ".com" files are rarely seen by users anymore.)
But if the .zip TLD takes off, it's just adding a little bit more cognitive load. Sure, hopefully it's usually clear whether somebody's discussing a filename or a domain name from context. But not always, and that's annoying and anti-user. Conventions have value, and this decreases that value.
So really, it's just like... of all the possible TLD's, is there really any benefit to picking ones that are also common filename extensions? Is our economy really going to suffer if we say, hey let's not make things like .txt and .doc into domains as well? There are tons of other TLD's we can create instead.