I think one of the problems is that while in Debian, pkg_resources and setuptools are separate binary packages, it's not entirely clear to me that upstream views them as different packages. After all, they are Python packages distributed in the same git repo and tarball. Debian's separation of them is a bit artificial.
You could solve this by promoting *-pkg-resources Suggests of *-setuptools to a Depends, but that sets up a circular package dependency since *-setuptools Depend on *-pkg-resources. In a sense I think that reflects the bootstrapping issues raised by upstream in GH#863. Does it ever make sense to install pkg_resources and not install setuptools? I'm not so sure, but collapsing them at this point is probably more intrusive than what we want. Another option would be to create new meta packages which Depend on both *-pkg_resources and *-setuptools and encourage people to Depend on that. Ultimately for this specific case, I think it's just easier if dput added a Depends on python-setuptools.
