Yeah, this has been brewing for years in Fedora. Overall the page is informative and correct and in particular it explains well why they chose to symlink /bin -> /usr/bin rather than the other way around. The only thing that annoyed me was:

The biggest part of Linux software is built with GNU autoconf/automake (i.e. GNU autotools), which are unaware of the Linux-specific /usr split. Maintaining the /usr split requires non-trivial project-specific handling in the upstream build system, and in your distribution's packages.

Well. You call ./configure --prefix=/ instead of ./configure --prefix=/usr. But maybe that's instead a bit of an oversimplification, and anyway I do buy the argument that higher uniformity among packages reduces the maintenance burden.