That article is about the Google Transparency Project, which is a separate organization from The Intercept. Think of GTP as being a PR firm and The Intercept as being a publication. PR firms work to place sources & articles with publications that they feel will be friendly to their message, but the publication itself is a separate organization that reports on many topics besides what the PR firm wants.

So as you mentioned, The Intercept is "friendly to" anti-Google messaging, which is exactly what I'm saying.