I would suspect that waterspouts occur in conditions with a recognised boundary similar to what occurs in landspout scenarios.
Generally, steep lapse rates until cloud base is another key indicator. In the case of landspouts, extreme heat at the surface achieves this. In the case of waterpouts, relatively warm ocean temperatures or extremely cold air aloft are often observed when waterspouts are observed. In all cases of videos that I have observed, a distinct boundary can be observed that the waterspout traverses.