Any idea how GitHub perform sync of PR branch with target branch?

When I traditionally rebase local branch against master I always get plenty of conflicts, contrary to GitHub branch sync with master gives only a few. I try to adapt my local gitconfig to the way Github do it while we want to sync PR branch with target branch.    Any idea how this is performed from merge/rebase and gitconfig perspective?  Any idea how GitHub perform "update branch" button action?

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