You can see on archive.org where it captured directory info for files which were not stored:

https://web.archive.org/web/20031218202130/http://www.sonic....

When you navigate those directory archives many of the files are missing. E.g.

https://web.archive.org/web/20030529230704/http://www.sonic....

Some design documents ARE there, e.g. "Specification of 3d display for starquest" : https://web.archive.org/web/20030719111039if_/http://www.son...