The KV store and search head clustering operate pretty much independently.
The KV store captain is elected by its peers, just like the search head captain, although it is different code that runs those two elections. It's possible that one node would end up hosting both captains, but not necessary.
The potential warning you point out is not a warning, but rather information about how kv store handles reads and writes. And where exactly do you think the docs are in conflict? KV store runs on a search head cluster, but search head clustering doesn't interact with the KV store.
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