I love graphene as much as the next guy, but this article is pretty terrible. Badly researched, just spitting out talking points that are either flat out wrong, not the point of graphene or just scratching the surface. Look up the graphene homepage, if you actually want useful info.

That’s a myth. Security of flatpaks depends entirely on the given permissions, and since most flatpaks just set their own permissions on installation, or require filesystem access to work, there is no meaningful difference in security OOB.