Very good idea for WordPress.com custom domain holders. Since it would be difficult for custom domain holders to use CloudFlare's free Flexible SSL offering, getting LetsEncrypt SSL automatically is a big plus. Since SSL is now a minor ranking signal, these sites will certainly see the benefits in SERPS.

I'm using CloudFlare's free offering on all my domains in a WP network on WP Engine. It's been smooth sailing for me on that front with SSL, but I do have to install the CloudFlare plugin and set an API key, so the WordPress.com offering is lighter, faster, and a great option for those custom URL holders.