I'm obviously biased (as tool creator) but I'd like to point out that copying configs is exactly the problem we wanted to avoid. It is hard to keep them up to date in different projects as tools evolve. You need to know which versions of which tools are compatible. Any time a tool updates, you need to do this work again: figure out migration instructions for each tools, update the configs, find latest stable compatible versions, etc.
On the other hand, Create React App gives you a single development dependency that encapsulates multiple tools working together. We ensure that they are compatible, and we do the work of updating the configs for you. In the rare case when there are breaking changes, we enumerate them in a single place with migration instructions.
Let me give you an example. Redux repo has a few example apps that are built with Create React App. At the time they embraced CRA, it was using Webpack 1. Then a few months later we released a version of CRA that uses Webpack 2, and adds many nice features (such as runtime error overlay). It was result of months of work from CRA contributors, and internal configs changed considerably, but it only took a few lines of version changes to migrate the Redux example apps to use it! And now we migrated CRA to use Webpack 3 in a patch release. So anyone can safely bump a single package to get all the build speed improvements. But if you used Webpack directly you'd have to watch out for breaking changes, update plugins to compatible versions yourself, etc.
I hope this gives some additional perspective for why keeping config separate might be a better idea than copying it into each project. Even if you don't use CRA, I hope you see benefits of this "shared config" approach and can apply it to your own tools.