I wish we could have something like exes with permissions. Similar to browsers. So I could run an arbitrary executable, but the OS level APIs would be blocked unless the user allowed the given permission.
The problem isn't the technical hurdle, it's that sandboxed apps really aren't what we want in a lot of cases. There remain a lot of use cases for native apps the interact directly with the hardware in ways that are hard to abstract safely. Games need the whole GPU, backend middleware needs the raw network stack, you want to set up routing tables or a custom NAS, etc...
Those requirements don't go away even when "most" stuff can be done in a browser-equivalent sandbox. And... you need to rely on your Linux distro for those things still, or at least compile from an active github project. You can't just get raw binaries from whoever and expect to be safe.
Flatpack and snap and other systems that conflate packaging and permission management get it totally wrong. Permission management is an OS-issue, not a packaging issue. Thus, distributing a plain static executable or a python script should be just as safe as a "safely packaged" app.