The things in PREREQ are required and then $VERSION checked for. The version specified using VERSION_FROM is retrieved by parsing the file. From the ExtUtils::MakeMaker docs:

Instead of specifying the VERSION in the Makefile.PL you can let MakeMaker parse a file to determine the version number. The parsing routine requires that the file named by VERSION_FROM contains one single line to compute the version number. The first line in the file that contains the regular expression

    /([\$*])(([\w\:\']*)\bVERSION)\b.*\=/
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