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I somewhat wonder if CloudFlare is issuing two different certs. An "internal" cert your servers use to serve to CloudFlare, which uses a private CA only valid for CloudFlare's internal services. CloudFlare's tunnel service validates against that internal CA, and then serves traffic using an actual public CA signed cert to public internet traffic.
Honestly though, I kinda think you should just go with serving everything entirely externally. Either you trust CloudFlare's tunnels, or you don't. If you don't trust CloudFlare to protect your services, you shouldn't be using it at all.
That's what I'm settling on. However, it's not just about trust, some of the services I'm exposing deal with moving files and I'm mostly interested in higher speeds associated with local transfers as well as not using up my internet data cap.
Here's a drawing of what I think might be happening to your private traffic: traffic diagram
One major benefit to this approach is CloudFlare does not need to revoke an entire public certificate authority (CA) if a singular private tunnel's Certificate Authority is compromised.