They're paying for access, not to keep Apple out of search -- otherwise they'd pay a few extra billions on top so that users on Windows can't use that potential Apple search.
Why isn't Google paying Microsoft billions per quarter to stop Bing? Because Bing isn't a threat, and neither would Apple Search be. What is a threat is Apple making it hard for users on iOS to use Google Search. That's what the money is for, it's the rent they pay to have their little shop in the walled garden.
Could you expand on what you mean here?