I think claiming that "SSH provides stronger security guarantees than X.509 certificates" is pretty outlandish.
SSH is trust-on-first-use. How many people actually verify the key fingerprints? Maybe you do when you're sshing to your single corporate bastion, or to Github.com, but could you imagine if you had to do that for every website? It simply would not work. It only barely does for SSH because of the (relatively) low amount of use SSH gets. When at a previous company I set up an SSH CA, we found an SSH MITM within 3 days (though benign; an ISP-provided modem/router was resolving all hostnames to itself when the WAN was down), and the user was planning on just accepting the new SSH host key.
Certificate Transparency is an auditing system, so of course it's after-the-fact. It has helped to improve the CA system immensely. While there's still work to do, the TLS ecosystem is unrivalled in terms of actual security benefit delivered to the most people.