applications – There’s some weird storage nonsense going on, as if part of an app’s data is permanent on your phone?

We can’t tell how you are freeing the storage. If you are using any third party app then it will free the caches of whatsapp. In which case no one can say how much storage is used by your whatsapp cache. Whatsapp it self deletes some caches when there is no need of it. So, if it’s cache then it’s totally normal.

Other than that you should look into Whatsapp’s media folder where all your images,audio,video and docs are stored.