Both APIs use the same authentication flow that lives under a kraken URL at the moment. Not sure I’d consider it a part of kraken as far as API versions go. The terminology I personally use is v3, v5 and Helix.
It’s also worth keeping in mind that Helix isn’t complete yet, as the roadmap shows there is much more work to the API on the way. I would hope part of those futures plans would be to have authentication done through a helix endpoint (or maybe just the root api.twitch.tv) seeing as v3/v5 is scheduled to be removed at the end of 2018.