Is that an 'undocumented feature' of Perl or what?

Actually, that appears to be a documented feature of Archive::Zip

Selected quote from Archive::Zip::FAQ.

Duplicate files in Zip?

Q: Archive::Zip let me put the same file in my Zip twice! Why don't you prevent this?

A: As far as I can tell, this is not disallowed by the Zip spec. If you think it's a bad idea, check for it yourself:

  $zip->addFile($someFile, $someName) unless $zip->memberNamed($someNa
+me);
[download]

I can even imagine cases where this might be useful (for instance, multiple versions of files).

See perldoc Archive::Zip::FAQ for further info.