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.
For anyone interested, a book was written on this about 15 years ago by a reporter from "Janes Defense Weekly".
"The Hunt for Zero Point: Inside the Classified World of Antigravity Technology".
Not as tin-hat as you might think, mostly a story of a lot of dead ends while trying to research some DARPA dark projects.
I really would say your just restating the OP conclusion from the point of the of the purchaser instead of from the point of view of the software developer.
An executive at an Enterprise would state their search for some piece of software as: I have such and such problem. I wish someone would make a magic wand and fix it for me(how hard can it be anyway).
To which some software developer will reply. Hey we make magic wands. We make incredible magic wands. Let's schedule some time to show them to you. And the fact that the people who have to use it are not involved makes a huge difference in quality.
You give Word, Excel and Jira as examples of Enterprise Software. If these are examples of Enterprise Software they are by far the best examples of such Software.
Enterprise Software that currently makes my life miserable on a daily basis would be products like Remedy for workflows and approvals, Serena and Harvest for Change Management, WebSphere Middleware, CyberArk for secrets management, and WebMethods for an Enterprise Service Bus.
All of these have horrible documentation, are extremely expensive, and most have superior open source equivalents.
The only reason that companies like this can still stay in business is because there are executives who still believe in magic wands and then believe sales people when they say they have them for sale.