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I don't have personal experience that can help. But, your combination is unusual and complex. While someone here may be able to help, you may find better luck at a different forum like for cert-manager, Cloudflare or perhaps K8s
Also, could you possibly use a Cloudflare Origin CA Cert instead of one from Let's Encrypt? You proxy your domain at CF so are using its CDN. Their Origin CA cert allows HTTPS between its CDN edge and your origin server.
Your setup:
K8s
cert-manager
a domain name proxied at Cloudflare
using DNS Challenge involving some sort of gateway
after I dig deeper it turns out i have a wrong set up in the yaml. I used cloudflare-api-token-secret as a secret name but in the refer i write it as cloudflare-api-key-secret
and after resolving that i found some issue that it should be used apiTokenSecretRef rather apiKeySecretRef