The only hard part about threading 'lite' comments is a stable parent reference, but we could use the first 8-10 bits of the tx hash for this purpose. The main reason I suggested non-threaded was for simplicity. It may or may not make sense to bundle these with votes (i.e. a comment with a up/down vote) or reactions, and nesting them makes less sense in that case.
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Couldn't the commenter include their own unique permlink-like tag in the json, pretty much the same as a regular consensus comment? The only real difference is tracking it in hivemind rather than steemd. You can't enforce that people put in properly-formatted json, but if they don't you can ignore it.
Yes, the only concern is that with this approach hivemind would have to track uniqueness of permlink/id's, and create/track a valid/invalid state on each. This opens up more edge cases and would make it harder to reimplement the protocol. Trx hashes are already unique, indexed, and part of core consensus, which makes them attractive to leverage.
I don't believe you need to actually store or track invalid state, just check that each custom_json is valid when processed. If the custom_json creates an invalid state (for example, presents a non-unique tag), the custom_json is invalid and is ignored. This is the usual method for doing any sort of embedded consensus, which is effectively what this is.
In fact, now that I think about it, non-unique might be considered as valid, since referencing an existing id could be an edit, if the rules mirror those for comment ops. In that case, there would be no invalid (non-unique) ids.