I'm not going to weigh in on the specifics of Flatpak vs AppImage, because I don't know enough about the particulars.

However, I think the "user choice" argument is often deployed in situations where it probably shouldn't be.

For instance, in this case, it's not the user's choice at all, but a developer's choice, as a normal user would not be packaging their own software. They would be merely downloading one of a number of options of precompiled packages. And this is the thrust of the argument. If we take the GitHub rant at face value, some developers seem to be distributing software using AppImage, to the exclusion of other options. And then listing ways in which this is problematic.

I, for one, would be rather annoyed if my only option were either AppImage or Flatpak, as I typically prefer use software packaged for my package manager. That is user choice, give me the option to package it myself; hopefully it's already been done for me.

There are some good things to be said about trust and verification, and I'm generally receptive to those arguments way more than "user choice."