For the static parse I rely on the "provides" list in the metadata. For the above example the Makefile.PL includes something like this:

my $release = '1.01';
my %MF = (
    META_MERGE => {
        'meta-spec' => { version => 2 },
        provides => {
            'Foo' => {
                file    => 'lib/Foo.pm',
                version => $release
            },
            'Foo::Bar' => {
                file    => 'lib/Foo/Bar.pm',
                version => $release
            },
        },
    },
    # ...
};
WriteMakefile (%MF);
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So the version is specified explicitly twice: once in the Makefile.PL and once in the master module. If there's a reliable way to specify it explicitly only once that would be good to know.