And third, initially the mobi version was in the periodicals form (not sure what it is like now) and some people like the normal book form better and this you can create with the script. The books, for example, you can place into folders on the Kindle, the periodicals you cannot. Also the navigation I like in the book form better.
And fourth, with the script you can distribute the paper to several kindles (e.g., in your family and/or on a kindle and a tablet), while the e-mailed one can only go to a single kindle.com address.
And fifth, the version that Die Zeit offers at least used to have a lot of typographic and other errors that can be corrected by means of Calibre's automated processing, which is what "my" changed version of one of the scripts that is offered here has been doing (along with adding the full first page as an icon instead of the cut-off version that it used to have).
Hope that helps.