Add a tone as an Alert Tone rather than as a Ringtone
As of iOS 11 it is not possible to create custom Alert Tones, only custom Ringtones.  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 &amp; 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.