We can and should still do that for people who want it (i.e. most people). The security conscious can decline to use them, but that doesn't mean the rest of us should have a worse experience.

But if you're just a "GIVE ME THE .EXE" person, how do you know the binary you're looking at is a legitimate network scanner or keyboard mapper or game cheat or whatever? You don't. You can't. You just followed a link from someone else who thought it was.

The basic point is that software in the modern world is too complicated to require regular users to validate. They can't do it. And so we need to have trusted authorities like distros and app stores to do it for them, even (especially) when they demand we JUST GIVE ME THE .EXE.

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.

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.