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.
It's an interesting question. One part of the the answer is that the idea is for there to be a single subtree off the root where "the operating system" lives. Where MacOS 10 has /System, OS/2 has \OS2, Windows has \Windows, and Digital Research DOS has \DOS, systemd Linux has /usr.
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.
A lot of those designs predated initramfs. I have yet to hear of a setup where there's a good reason for not mounting /usr in the initramfs. (Though, yes, I have heard of setups where you can, it would just be a fairly involved change. It is a legitimate problem for these sysadmins to be compelled to rearchitect things, although I'd personally blame that more on the distro model where all parts of userspace are tied together than on systemd itself.)
