Comment # 3 on bug 976196 from Stephan Kulow

you can use /usr from anywhere just fine - the initrd will mount it for you
before it starts the system. If there is a real problem with it, please attach
the logs. What you did is invalid as you need to setup the system like this and
not change it afterwards. The FHS does *not* state that you can get rid of /usr
in a running system - only that you can share it.