But that’s not the point that is made against flatpaks - the point made in the article is “it allows access to the home directory, so it’s worse.”
Whether flatpaks is better or worse than packages depends on many other factors. Flatpaks allow software providers to package for multiple operating systems in one package, for example. This makes software available that otherwise wouldn’t be. Whether that’s worth it or not is debatable, but raising clearly invalid points to attack flatpaks is disingenuous.