If a package is only supplied in autopackage format, you must not add it to the tree. If a package is supplied in autopackage format and some other sane standard format (for example a source tarball), use the other format only.

Autopackage packages are totally unsuitable for Gentoo systems for a large number of reasons:

Upstream are aware of these issues and have no desire to fix them — indeed, they pass off some of their most broken behaviour as 'features'.