Earlier quoted context omitted.
/usr/share/nginx is the default root path for nginx. It sounds like Ubuntu has just stopped trying.
The docroot path? That would indicate the Ubuntu devs who chose this location had little or no sysadmin experience. Files and dirs under /usr should not be mutable, that's what /var is for. At least they didn't locate it on the root directory. Mount points should never be on root. See the sources for stat() for the main reason why not.
I don't understand. I have /boot, /home and sometimes /srv in a different partition. I don't know of any other way to accomplish that without using putting mount points on root, unless you mean additional, non-FHS mount points...