Indeed, a CT monitor which sends alerts about legitimate certificates is almost useless due to noise. My service, Cert Spotter, provides an API endpoint[1] which you can upload your CSRs to, so you don't get alerted about certificates using the same key as the CSR. The open source version of Cert Spotter can invoke a script[2] when a certificate is discovered, and the script can cross reference against a list of legitimate certs.

[1] https://sslmate.com/help/reference/certspotter_authorization...

[2] https://github.com/SSLMate/certspotter/blob/master/man/certs...