I thought I knew what the author meant until I got to the end. I could be that they're referring to HTML as one API, and JSON-RPC as the other API.

Originally I thought they meant 2 JSON APIs. One that's tightly coupled with the HTML to handle all the "ajax" requests, and the other for 3rd parties to fetch arbitrary bits of data.

Otherwise, I know what you mean. My company has our internal RPCs and then our customer-facing API and the customer one hasn't been updated in ages and it's just a thin layer over some old internal RPCs we used to have and now we have to maintain backwards compatibility but keep breaking it anyway.