Why is /usr/bin being adopted as the place for binaries with /bin linking to it instead of the other way around? Since they're essentially the same directory under this setup why not favor the short path?
In short: because having things in /usr is equally compatible, and makes some useful things like atomically snapshotting /usr to snapshot all executables, mounting /usr readonly, etc. possible.
Of course, another part is that this is an old idea, already implemented once in the commercial Unices a quarter of a century ago. They merged /bin into /usr/bin, with a symbolic link from the former to the latter.
But it is this kind of stuff that they are trying to change (as usual for systemd, without fully thinking why people do it differently now).