Hi, Kopia author here.
Yes, Kopia does segregate metadata from data. Directory listings, snapshot manifests and few other minor data pieces are stored in pack files starting with "q" while the bulk of data is stored in pack files starting with "p". Indexes into both kinds of pack files are stored in filenames starting with "n".
This has some interesting properties. For example we can easily cache all metadata files locally, which provides fast directory listing, manifest listing and very fast verification without having to download actual data.