With Let's Encrypt we will basically have to trust DNS.
Check DNS with Nir Sofer's tool: DNSDataView (combined with his tool IPNetinfo).
Online check with: DNSSec Analyzer dnssec-debugger.verisignlabs.com
and re-check with DNSViz at dnsviz.net
(Mind you that at dnsviz.net you will also communicate with twitter,
lest you haven't blocked that with NoScript for example)
Check for twitter searching nitter.eu or nitter.it).
Important to check DNS, because certain Android-malware may change DNS-settings.
Be vigilant,
polonus