"Packaging" in this sense is putting together a set of application-level scripts, configuration files, etc. in a form suitable for distribution and installation. In other words, I am using the word "package" in one of its common English senses and not in its Perl sense.

If I'm not mistaken, in Perl (5), every module is a package, but not every package is a module. The "package" keyword simply defines a non-default name space in which to put variables, functions, and/or methods. It can be used within an ordinary script, but is usually used at the top of a module's .pm file to define the name space of the module using the module's name.