It sounds like the way forward will be for new feature specs to explicitly define their comment types. Kind 1 or kind 1111 could be used as a baseline, with additional requirements added to support the needs of the intended feature.

The potential pitfall is that clients would have to reimplement basic comment support multiple different times for different feature sets, but I don't think that's necessarily such a problem. Nostr apps don't need a "global" feed that sucks up everything, nor does every client need to support most NIPs. Make more single-use clients.