I took another crack at this one, and it is proving to be quite annoying. This seems to be an issue mainly with the version of the assembly plugin we use. However upgrading just leads to more issues.
I think the issue mostly lies in that we don't do a full assembly for our releases. However doing so we would have to redesign how we build the artifacts, so a bit of work.
Anyways, I am going to push this back and for now just going to supplement the release docs with a step that includes manually stripping out the directories.