The App Store is based on webViews to easily update the store on iOS devices and desktops (iTunes, web) So the search results and charts as well as highlights in the podcast app might be presented as web views too and therefor can't be displayed properly in different size classes.
Usually apps that use size classes and have the ability to be presented in split view should provide a great UX for all sizes. Also, I would expect Apple to adapt their own apps for multiple iOS-devices with size classes.
If you're using a native app, this app only lives on the device(s) which is was developed for. So there should'nt be any restrictions in terms of the experience, no matter on which size class the content is presented. It is different with responsive websites though since you can view the site on so many different devices, have different load times and you should'nt display all content on all devices - The content should adapt to the device it is presented on.