How do you suggest the email challenge be automated?
Since Let's Encrypt certificates only have a 90 day duration (and may be shorter in future), it seems contrary to the mission for Let's Encrypt to be an "automated" CA:
Automatic: Software running on a web server can interact with Let’s Encrypt to painlessly obtain a certificate, securely configure it for use, and automatically take care of renewal.
There are CAs in the wild that do support automated renewal after initial validation via email (since as Amazon CA via Amazon Certificate Manager), but due to the integrated nature of their platform they are able to prove domain control at renewal time in other ways. Let's Encrypt can't do this, and it has been looked into previously - they don't want to.