I’ve spoken to the relevant team, and the reason the Deploy a Package step does not support jar is that jar files are not always zip files and can require Java to be installed on the destination for extraction.
We also did not anticipate that jar files would be used in a manner compatible with the Deploy a Package step. The Deploy Java Archive step will re-package the jar correctly after applying transforms.
Are you expecting the files to stay extracted on the destination server (which is what the Deploy a Package step does? Are you able to use tgz or zip files instead? If not we may consider allowing the extraction of jar files in a future version.