My understanding for having /bin, /lib, /var and /etc on root file system level and not in /usr was that absolutely essential OS tools could reside, if necessary, on a very small file system usable for all rescue scenarios, without the additional bloat of all the additional (but non-essential) software in /usr. This allows to put /usr on a separate disk. Even with today's disk capacities, this seems not a completely outmoded concept. It still makes sense, in many scenarios, to put all root directories on a small but fast SSD and /usr on a slower but bigger hard disk.
I wonder why one would throw out such a sane design.