The permissions are per-user, not per-app and that is the problem. The distibution developers assume that you trust the programs you run, but how can I trust commercial and proprietary software? How can I trust the code from a random guy on Github without a passport verification?

Depends on your setup, you can have per-app permissions too. Flatpak, snap etc do this for desktop apps, Android does it, containerized server apps do it. But of course if it turns out you're running malware, you're going to have problems when it transpires that you've delegated something valuable to it, even if it doesn't break out of its permission set.