Currently for ZIP files PlexusArchiverZipFileResourceCollection is used and PlexusIoZipFileResourceCollection for the rest of the ZIP based file formats (Jar, War, etc). Apart from being inconsistent, there is performance penalty for using PlexusIoZipFileResourceCollection (see codehaus-plexus/plexus-io#12).
According to this comment there are integration tests in Maven Assembly plugin failing when PlexusArchiverZipFileResourceCollection is used for all formats.
Does anybody knows what the issues with PlexusArchiverZipFileResourceCollection are (if there are any - there were some bugs fixed since)? /cc @krosenvold