Downsides of Flatpak

One huge thing I don't understand about Flatpak is how, like the article says, everything is shoved into GitHub. Why? What is the rationale behind making each application its own repository just to store a couple modules and a YAML file?

I do like Flatpak though. It works for what I use it for, and it does a good job at keeping the applications I install through it separate from my system, so I can be sure that my package manager isn't going to brick everything with an update (not like that has ever happened though).