Yeah this is a tricky problem, and it's one of the reasons we updated our recommendation to use a framework like Expo that can make upgrades be smoother by being more opinionated about the setup.

As the core library, we need to support all the different ways React Native can be added to an app (from fully react native to adding react native to an existing app) and all the different build tools an existing app may use. So it's hard for us to be opinionated about the setup in a way that would make upgrades seamless, but a framework can solve this for you.