From what I have seen, the downloaded archive should be repackaged, otherwise Wrye Bash will not detect (and therefore not install) the .esp file of SSE High Quality Music's optional version! :/
You are correct. The music still installs just fine. Users will simply not have the restored content unless they repack or install in MO/NMM and archive the installed mod from there.
I will repack this for the author and offer it up.