Control over a nonstandard port on a server doesn't necessarily mean that you control the web server on :80 and :443 of that host. For example, a nonprivileged user can listen on :8443 and get a cert.
Well, there are ports that require root to bind to that aren't 80 or 443. That being said, I guess it's relevant here that Let's Encrypt only supports certs for HTTP use cases.
Which leaves the question which one to occupy instead. There was the suggestion on the mailing list of officially getting an acme-port reserved, but I don't remember if there was any follow-up.
The problem is not all systems are *nix. Windows doesn't enforce the <1024 port restriction. The advantage of using port 443 I suppose is that it's so commonly used it'll probably (maybe) be tied up with one service or another when it comes to any important host. I guess. But really it's all guesswork and hope when it comes to deciding how to validate host control.
