In my mind the principal reason for the current hierarchy is read/write usage. With /etc and /usr it is possible after installation and configuration to set one or both as Read Only. With /var and /home you have the directories that should be Read/Write on a running system. This allows you to mount each of those directories on a different partition with different settings or even different filesystems depending on how you want to optimize/secure your application.

Now admittedly actually doing this is pretty rare in these days, but I still like having the option. I believe he does address this talking about "union mounts" and "overlay filesystems". I'm really not too familiar with either or how production ready they are, but it may address my concerns.