Also note that your domains are live as they're allocated (they exist). Whether a web server or anything else actually backs them is a different question entirely.
For "secret" subdomains, you'll want a wildcard certificate. That way only that will show on the CT logs. Note that if you serve over IPv4, the underlying host will be eventually discovered anyways by brute-force host enumeration, and the domain can still be discovered using dictionary attacks / enumeration.
Never touched Cloudflare so this is as far as I can help you.