If you make a new app with exp or XDE, the new app will be created with the Expo fork of RN. The Expo fork includes some bug fixes and new APIs. It’s backwards compatible with the corresponding upstream release.
If you use CRNA, a non-forked version of RN will be used. This is usually totally fine and won’t have any effect on your app, and so you don’t need to worry about changing it unless you encounter a bug that’s fixed in the Expo fork or need some API that’s only available in the Expo fork. The fork is very thin and is almost exactly the same as the vanilla react-native JS lib, but is occasionally useful.