The problem is flatpack/appimage are equally bad/opaque, they solve one problem at the expense of being better off just in windows or osx.

tar.gz is opaque in a different way - the solution would be more like an interpreter - something which has a good guess how you should install/run the file.

There is the issue also of integration with the distribution, this is a problem with distribution apis - package maintainers are invested in their formats and distribution list not solid apis with which to interact. If you could build against such a set of Apis you could bundle an interpreter which just knows what to do.

Tar.gz is a hell of a lot simpler than any other format, it's not the issue, it's the desktop distros who are underfunded/at fault.