Webpack build vs react-scripts build
Webpack is a general purpose bundler, with applications beyond React. Before create-react-app, the web was full of examples of setting up a brand new React project which uses webpack as the bundler. It is extremely flexible and can handle things including and beyond what a React application would need. It works for Angular, Vue, NodeJS and even Web Assembly.
But it used to take a while to setup. You will need to understand its working and configure it so that you can transpile your React+ES6 code into plan-vanilla JS. You would need to decide the output structure you like and configure webpack for it. And then also add hot-module-reloading and code-splitting support yourself. During this, you will also need to add other plugins required by Webpack to support all the above :).
This naturally caused some fatigue with folks who were starting with React.
So facebook created cra which internally uses webpack, pre-configured to include all the nice tools to take care of these basics and help you focus on the React part of your code. It hides webpack from you as much as possible, otherwise the build process may break if the configuration is changed by the user.
With that aside, the structural conventions which cra uses should not be having any performance impact over a bare-bones webpack setup. It's just a convention.
Your question should then be, when would I use create-react-app and when would I use Webpack?
As a beginner you might want to stick to cra as you focus on your react app. Eventually there would come a time where what you want to do is not supported by the webpack configuration cra is managing under the hood. A very common example is if you want to write a component library to reuse in other apps. This cannot be done by cra (it's about the whole app :)). You can then switch over to webpack and start learning it.
react-scripts hides all of the webpack configs behind the scenes. The advantage of this is it makes it cleaner and since create-react-app is regularly updated, its easy to stay up to date with React, Webpack, and Babel. The community automatically fixes the issues for you.
In terms of performance, should be the same regardless with react-scripts or with webpack.
Advantages of running only webpack:
Full control of your environment
Can do custom things like server-side rendering easily (still possible with
create-react-appKnowledge of webpack as a skill
Disadvantages of webpack only
Full in charge updating and maintenance of webpack (some webpack versions are not backward compatible or future compatible)
Can be intimidating and can be a headache if you are trying to learn to react quickly.
If you want to customize create-react-app, here is some info
https://auth0.com/blog/how-to-configure-create-react-app/
Here is server-side rendering with create-react-app
https://hackernoon.com/server-side-rendering-with-create-react-app-1faf5a9d1eff
TLDR: Use create-react-app / react-scripts if you want to go to 0-100 as quick as possible for whatever reason
Use just webpack if you enjoy messing around under the hood