Well, with a rebase workflow, there should be no merge conflicts during the final merge. That should always be a fast-forward.
Of course, that’s because you shift those merge conflicts to occur earlier, during your regular rebases. But since they’re much smaller conflicts at a time, they’re much easier to resolve correctly, and will often be auto-resolved by Git.
You’re still right, that if you’ve got a long-running feature branch, there’s a chance that a conflict resolution broke a feature that got developed early on, and that does become invisible. On the flip-side, though, the person working on that feature-branch has a chance to catch that breakage early on, before the merge happens.