The PKI in this context is just the platform that is managing the issuing and revocation of certificates not the underlying algorithms being used, if that's what you're asking.

So the LE systems that accept, check, and approve the initial request, and then handle the revocation when needed. Using a different stack for different use-cases is a best practice, simply because if one is compromised, it doesn't affect the other. In this case it's just splitting the standard LE web services and TLD services into two different stacks that do the same thing, but I assume would have isolated CAs, one for each use-case. This would mean a new root CA needs to be deployed out into the world in order to verify the TLS side, but maybe I'm missing something.