Yeah there was definitely some back and forth about it before we were eventually approved.
In a sense, this isn't very different from what React Native does (run interpreted code that calls out into native code), just with Swift instead of JavaScript. There used to be JavaScript-specific requirements in the guidelines, but that has been loosened since Swift Playgrounds was released. Now there are Python IDEs, Jupyter Notebooks, and other apps running arbitrary code in the App Store.
The root of these restrictions is to try and prevent people from using dynamic code to bypass App Store reviews. If you're planning to change the functionality of your app then you must submit it for review.