The goal of create-react-app and react-scripts is zero-configuration React development. The less time you spend configuring development boilerplate, the more time you spend developing components. You should continue to avoid worrying about configuring your app for as long as you can. But at some point, you'll have to bail on create-react-app and maintain your own configuration.
Providing a zero-configuration environment is only possible because many defaults and many limitations are assumed by create-react-app. This is the trade-off. By providing sane defaults for most of the things that React developers have to do but don't want to, you're making a choice for the developer. This is a good thing—being able to ...