> here's not even a hint that their system works in OSes other than Linux.

> And there's absolutely nothing there to suggest it supports Windows/IIS.

Their "system" is an API for issuing certificates. There's nothing platform specific about that.

> right now the website conflates the two badly.

From https://letsencrypt.org/getting-started/: You’re welcome to use any compatible client, but we only provide instructions for using the client that we provide.

Edit: This is the protocol they use: https://github.com/letsencrypt/acme-spec

I found the link here: https://letsencrypt.org/how-it-works/