Off the top of my head, I'm sure I'm missing a few obvious ones. Notably CRA doesn't prevent you from doing any of these, but taking the time to learn the various build tools will better enable it.

* spend less time debugging dependencies across version changes

* reduce bundle sizes

* create a better CI/CD pipeline

* reduce unnecessary dependencies

* fork/fix/create your own plug-ins and other tools

* self-hosting npm to avoid production/dev outages

* easily learn new tools because you understand the underlying systems/alternatives