The article is simply just factually wrong.
Cloudflare runs onion services for every site they host, to tell apart Tor circuits (as in by the unique id chosen by the client, not by some unintended means).
Connecting a clearnet site looks like this:
You → Guard Relay → Relay → Exit Node → Website
On the other hand, an onion service is different:
You → Guard Relay → Relay → Rendezvous Relay → Relay (optional) → Guard Relay (optional) → Hidden Service
The optional nodes can be disabled, and in this case the Hidden Service is ran by Cloudflare. So the final chain you end up with is
You → Guard Relay → Relay → Rendezvous Relay → Cloudflare
I’m pretty sure in my math skills, and no matter how I count, that’s three.
And this operation is not exactly a secret either, Cloudflare even has a blogpost about it that apparently the writers of that blog post didn’t bother to read: Introducing the Cloudflare Onion Service
If I were you, I’d discontinue believing anything from that site.