Let's bump this thread, by mentioning a piece of software that is taking a new view on the hierarchy: systemd.
man 7 file-hierarchy describes a "modern" Linux hierarchy for systems that want to use systemd.
There isn't anything especially new in this hierarchy other than it including the XDG and systemd dirs.

What's new is that issuing systemd-path would help find where is what. For example to get the $PATH instead of the environment variable you can do:
So now there's a disconnection with environment variables and instead we have a centralized mechanism. Software don't have to be preloading env anymore.

The decoupling is advantageous in a sense but it is arguably very Windows registry-like in my opinion and probably comes with the same issues. And as with all systemd software you definitely feel the eagerness of wrapping everything under an abstract "micro-service-like" framework so that you never touch the underlying system.