Response from a Flatpak package maintainer - https://theevilskeleton.frama.io/2021/02/11/response-to-flat...
I'll leave others to make their own minds up, but I personally think the original article is FUD in a similar vein to some of the SystemD and Wayland nonsense that gets upvoted occasionally.
I use Flatpak extensively and I fully agree with you and the author of the response that there is a need to balance practicality vs. idealism when it comes to (fully auditable) FlatPak apps, as well as FlatHub's overall approach and continual work within the desktop Linux ecosystem.
What's more, the fact that an entire domain was devoted to what could have been a blog post gives credence to the responder's notion that this is FUD which, while valid for discussion, is most certainly not beneficial to the FOSS community writ large.
Either way, from the article you linked TIL about Flatseal[0] so I'll be taking that for a spin!