The way to arrive at the optimal system is to continually optimize all individual components as the system develops. You have to walk the razor’s edge between “premature optimization is the root of all evil” and not optimizing anything until it’s too late and a bunch of bad design decisions have been baked in.
If you want to write the fastest program, profile its performance from the start and try different ways of doing things at each step of the process. There’s usually a way of doing things that maximizes simplicity and performance at the same time because maximum performance == doing as little work as possible to complete a task. Chances are that ‘littlest amount of work’ will be elegant.
One properly and three half-flat tires on a car is an obvious visual here.
The counter-argument is that one must begin somewhere; waiting until everything is "chef's kiss" might mean much waiting.
Much has been written about failed overhauls. Even a great idea can fail because it's hard to run an old system and its replacement at the same time.
I don't disagree, but I really hate that it's not wrong. It keeps me up at night, frankly.
The seemingly most successful companies I have worked for have had tons of the most incompetent people doing the most bureaucratic bullshit. I'm not sure it can be blamed on "synergy" though as much as bureaucracies liking to give money to other bureaucracies making the whole thing a self supporting bureaucratic ecosystem.
I'm not sure if it should be taken as something to reach for as the article implies or a cautionary principle.
Given the choice I'd certainly rather work for the first company.