AllAs of iOS 11 it is not possible to create custom sounds are always added as RingtonesAlert Tones. You can’t define them as, only custom Alert TonesRingtones. iTunes iTunes itself only makes one Media Kind available for them: Ringtone. That cannot be changed.
You can assign both Ringtones and Alert Tones to any event under Settings → Sounds & Haptics on your iOS device.
As far as app-specific limitations are concerned, you’ll have to take it up to the developers of such apps, in this case WhatsApp. I doubt Apple will add that functionality, since it makes no difference to iOS itself.