What if you need to do configuration in Xcode?

I believe you could do it by writing a config plugin[1] that will apply the desired config changes to the native project files. Expo will apply the config from plugins when they are building the native app for you.

(Disclaimer: I use Expo at work for cross-platform app including web but never wrote my own plugins)

[1]: https://docs.expo.dev/config-plugins/plugins-and-mods/