dnf/RPM is the biggest offender in his benchmarks when it comes to package manager speed. Not only is metadata for a package an order of magnitude larger, the package manager itself works slowly.
Yeah. There have been multiple projects, even from inside Red Hat, to try to switch away from the text-based Berkley DB to any sort of reasonable database ( one example was razor: https://github.com/krh/razor ), but for a variety of reasons, it was never able to be dethroned.