I suspect the idea is that if all binaries are in /usr/bin, one doesn't have to fuss about where the binaries are. :) And if /usr is mounted early enough, why not? (There are some other benefits, like /usr being easier to set up than / as a read-only filesystem.)
I don't know of any systemd bugs in this area, other than a strange altruistic propensity to warn in its log about /usr not being mounted early enough for the sake of other packages like udev.