What is that one use case? What are the others that don't fit?
There are folks who like to live on the bleeding edge, and for those using something else (or ejecting) might even make sense... maybe. But for any production app you should just use CRA, otherwise you will find yourself explaining to your new hire all the obscure choices you made a year or two ago. Believe me, I've been on the receiving end of these explanations and it sucks.
CRA has its place, certainly. But it is a black box, and somebody in your org should know the tools well enough to make good decisions to build up a product from scratch without CRA... and then you may still choose to use CRA, but it is an educated choice, not a default answer because you do not know any other options.
Yes, 100%, if you have more exotic requirements from a bundler or build toolchain then you'll need to look elsewhere and probably have to start learning tools like Webpack in more detail. I try and avoid those requirements.
For example, on the reactjs.docs, https://reactjs.org/docs/create-a-new-react-app.html, create-react-app is simply one of four toolkits recommended, along with countless others in open source land.