The deprecation of setuptools is a joke. There's no replacement. What PyPA does is that they produce ever more bullshit wrappers for setuptools pretending they are doing something new.
I think that by "apt packages" you mean DEB packages. As someone who has to package a lot of Python both for RHEL and for Debian-like... well... so far and in the observable future, setuptools isn't going anywhere. On the other hand, I could easily do without it, and sometimes do. But it's not because PyPA produced any replacement to it. It's because I simply grow frustrated with how bad of a tool setuptools is, and I just write my own.
The claims PyPA makes about setuptools are because nobody wants to support that project anymore. It's awfully written at every level, from the minutia of formatting and up to the high-level design decisions. The problem is that everything else that PyPA came up with so far is a joke. The only reason I keep paying attention to it is because I'm being paid to fix problems created by using it.
I'm also going to tell you a secret... well, of sorts. DEB, and RPM too are also pathetically bad... since you seem to have some experience with DEB -- to assemble this stuff you typically have to use a bunch of Make macros. Excruciatingly painful to debug. Virtually no documentation and very few people who could help you if you have a problem. And, when it comes to Python packaging, things also changed over time. Not so long ago I saw some write-up about how to package Python including virtual environment in the package. In truth, if I were a distro maintainer, and someone came to me with a package like that, I'd told them to try elsewhere. It's a sign of disrespect to the efforts of the distro maintainers to assemble a working and coherent system. But, guess who does stuff like that? -- big companies, like Amazon or Microsoft. Instead of spending effort to figure out how to play nice with the distro's packages, they distribute a huge blob that's not humanly possible to audit.
I’m all too familiar with how difficult it is to create a DEB package from scratch. I honestly can’t belive how difficult it is to create what is really just an archive.
