If PAUSE honors both, then you should be able to use whatever you like. I haven't followed closely the changes in how the indexer works and what new features the META* files provide.
I like keeping one version number across a distribution because that makes it really easy to trace back from where a file originated. There is no room for confusion because I never have to remember whether version 0.17 of Foo/Bar.pm had the change that is needed for Foo/Baz.pm v0.38 , and both of them were distributed starting with Foo/App.pm v0.42 in the 0.42 version of the distribution. This is true for me for both "public" and "private" modules, because when trying to track down an error, it's much easier to ask the other end "What is the version number in the file?" than "What version of the distribution did you install?". Often, a module was installed as a prerequisite so the other end does not even remember explicitly installing a module.