Question re: Downloaded .zip file contents

When I looked into the WP download and the WP-Members download .zip files, I noticed several duplicate files of different sizes. If I unzip on my pc the OS will ask what to do with these duplicates.

e.g., for WP duplicates are 404.php, about.php, admin.php, archive.php, author.php

and for WP-Members the duplicates are index.php, users.php

What criteria do I use to decide which copy I should use ?

Thanks in advance for the help.