If I'm reading the settings page right, Chrome trusts over 70 certificate issuers right now. Let's Encrypt is just one of those, and only issues a limited set of certificate types.
As I understand it, Chrome (unlike Firefox) does not ship its own root CA store - rather it defers to the root store of the operating system that it's running on. It does however apply some form of blacklist / additional restrictions over what the OS may allow.