Who is publishing this list of possibly not-published-anywhere-else SSL sites? Having them all in a big easy to download list is not what I expected from LetsEncrypt.
It’s intentional. The general idea is to make it easier to detect fraudulently issued certificates. LetsEncrypt submit all certificates[0] to Certificate Transparency[1] logs.
Chrome won’t actually show the green address bar for EV certs unless a CT proof is provided along with the certificate[2].
Certificate transparency makes it much harder to surreptitiously issue a certificate and holds the offending CA responsible in case of unauthorized certificates. If your site is not public, you're better off with your own private CA anyway.
Also the server for LetsEncrypt is open source [1] and comes with test scripts to run it during development and testing to avoid premature exposure to the public instance of LetsEncrypt.
https://whois.domaintools.com/crt.sh
Thought I recognised the favicon, it's Comodo.
I don't see the problem, if you want a secret url then self sign and distribute your certificate with other methods.