It's really common for games to be able to download data updates without going through the app stores. Particularly those games that have small download sizes <100MB so that they can be downloaded over cellular connections, but when you first run them they install another 400MB of data. Even games that don't do major data downloads will often phone home and download configuration files to allow developers to change non-IAP shop prices, or modify difficulty levels etc.
You can't modify your executable without going through the proper update channels. However, if your game relies a lot on scripting, then the lines between executable and data are more blurred. I think the app stores are happy enough for you to patch or tweak your game outside of their proper update channels, but not to radically change it.
As Apple say in their
https://developer.apple.com/app-store/review/guidelines/: "We will reject apps for any content or behavior that we believe is over the line. What line, you ask? Well, as a Supreme Court Justice once said, "I'll know it when I see it". And we think that you will also know it when you cross it."