If you read the actual rule the exceptions are relatively well defined. Stuff like pythonista falls into their educational/coding app exception as they define it

The entire rule is as follows:

Apps should be self-contained in their bundles, and may not read or write data outside the designated container area, nor may they download, install, or execute code which introduces or changes features or functionality of the app, including other apps. Educational apps designed to teach, develop, or allow students to test executable code may, in limited circumstances, download code provided that such code is not used for other purposes. Such apps must make the source code provided by the app completely viewable and editable by the user.

There are not "exceptions"; there is one exception, and that's educational apps. But it's unclear why Pythonista is educational while the apps mentioned in the article are not. In fact, Pythonista is even listed in the "Productivity" section in the App Store.