apt has significant limitations vs. a more flexible package manager. I would never use an apt-based distribution; I would use a Paludis-based distribution: see its feature list for many of the reasons why.

Bloat is a concern because I don't want unnecessary system processes running, nor do I want cruft installed that can be done without. Gentoo is good at minimizing cruft, and others in the same spirit as well.

Can't help you with systemd and GNU, as I am comfortable with both.

The writer seems more like a Gentoo or Exherbo or Arch user than any of the more popular distros. In other words, one of the people who used to use Linux when it wasn't as mainstream.