An appropriate tone would be to press the angle that help is needed and either offer to help patch the applications or mention where contributors can get started.

I get the author's concern but there is nothing useful in this article. It's misleading suggesting that the problem is with flatpak when the problem is that certain applications aren't using its full capabilities, aren't configured correctly and are in need patching. Or in the worst case, might need a redesign to fit the sandboxing model. This needs to happen with any sandbox that uses this model, not just flatpak. There is nothing else that can be done about this short of suggesting users switch to a different sandboxing model like Qubes. (Maybe the blog author can try that too and see how it goes, or could develop their own sandboxing model just to see how hard it is on a complex system like Linux)