Strawberry Perl and Active Perl have very different concepts. Active Perl does their installation and integration into the system more or less completely "the Windows Way", while Strawberry's way is much more "Unixy", hence the different folders. It's difficult to compare them.

However, I think what you want to achieve is very similiar to what PAR::Packer and its utility pp does. Even if you dont want to create an EXE (see e.g. EXE from Script (Re: General advice desperately needed)), perhaps it helps you finding out which components you need.