That's not a modern problem and it's not something the developers did. If you have N apps and M themes, you have to test N × M combinations. This is an impossibly large number on any platform that allows users to make their own apps and themes.
It's a lot easier for everyone if the app developers decide they're only going to support a small number of approved themes, or if the theme developers decide they're only going to support a small number of approved apps.
It's a lot easier for everyone if the app developers decide they're only going to support a small number of approved themes, or if the theme developers decide they're only going to support a small number of approved apps.