I am not completely happy with the current way. It is not so nice that in 5.2 the versions.cfg gets you everything, and in 6.0 you only get the core versions. In this late beta stage I don't want to change much, but on the other hand it is not nice to have to support a suboptimal solution for years.
A versions-combined.cfg could be an option, indeed. Should be fairly straight forward to generate a full list of all versions during the release. Or are you thinking of a small file that simply extends the others? That could work too.
I am also thinking about having a versions-plone-core.cfg that really only contains Plone and its dependencies, probably not even extending the Zope versions files. Especially I think this should not contain zc.buildout, pip, setuptools: we leave that up to whatever the user is comfortable with. Currently we force a slightly older pip because buildout has a problem with the latest versions. We would avoid that.
The danger is that, combined with the Zope files, we end up with ten versions files and no one has any idea where a package pin should be.