The author points out systemic issues with Flathub, why it needs to improve, and then, through some crazy rationale, still recommends it because:
Although Fedora Workstation works well for most users, and although quality and reliability has improved considerably over the past decade, it is still far too easy for inexperienced users to break the operating system
Without stating "how" it is too easy for this to occur. Flathub is not a "fix", it's a host of other problems, many of which are in the article itself.