We have a single org-level webhook in GitHub Enterprise that notifies our Jenkins master (and our backup master) as to changes in all the repositories within it, but we do not utilize a GitHub Organization job on the Jenkins side (in order to have more control over per-repo Multibranch Pipeline settings like clone settings, build retention, etc.). Instead of a GitHub Organization job, we have individual Freestyle, Pipeline or Multibranch Pipeline jobs as each team prefers. However, every new Jenkins job that leverages this org-level hook to trigger its builds still causes the "There were some problems while registering or removing one ore more GitHub webhooks. Would you like to view the problems?" warning, despite the "Manage webhooks" checkbox being unchecked in the Jenkins configuration.
I see no benefit to having repo-level Jenkins hooks on the GitHub side (given this single org-level hook) and no desire to add another account with Admin-level rights on all the repos (as hook configuration requires), so have no need for this warning telling me about it. I've built up a long list of ignored warnings (per repo/job) on the GitHub Hooks Problems page, but it would have been preferable not to get these warnings in the first place.
Is there a benefit I'm missing to repo-level hooks in this case, or a way to suppress these warnings more generally that I'm not seeing?