You are right to say that conflict analyzer tries to treat commits independently based on the service or app (which are usually in separate repositories in a multi-repo world). However, note that the problem of conflicting changes (or a red master) exists even when you are in a multi-repo world as you could have one repository getting a large number of commits.

In fact, at Uber we have seen that behaviour with one of our popular apps when we did not have a monorepo. The construct of probabilistic speculation explained in the paper applies even in this scenario to guarantee a green master.