When you look at the github repo for the gemini CLI:
https://github.com/google-gemini/gemini-cli/tree/main
At the bottom it specifies that the terms of service are dependent on the underlying mechanism that the user chooses to use to fulfill the requests. You can use code assist, gemini API, or Vertex AI. My layperson's perspective is that it's positioned as a wrapper around another service, whose terms you already have accepted/enabled. I would imagine that is separate from the Gemini app, the settings for which you linked to.
Looking at my own settings, my searches on the gemini app appear, but none of my gemini API queries appear.