I thought the whole point of the acme client was that the private key never leaves my server to go to let's encrypt servers. Now yes, if I am using cloudflare tunnel, I understand the tls terminates at cloudflare and they can share with anyone but still it has to be a targeted operation, right? It isn't like cloudflare would simply share all the keys to the kingdom?

Yes. They could issue their own certificates, but we have CT to mitigate that, too.