Ok, so from that it should work perfectly, but clearly that’s not the case.
I’m running low on suggestions, for some reason your IIS server is responding and therefore your content management system is responding with the 404 page. You could try restarting the Certify background service and also end any Certify tasks if there are any hung processes.
Do you run any other web server processes (like Apache or nginx) on the same server - that could prevent the http challenge server binding although I would expect the Test to fail if that was the case.
Is there anything running in front of the website like cloudflare or a load balancer?