“What is the correct way to handle redirectors for assets referenced in bundles?”
They should be handled for you by the CoreRedirects and the loading system. You shouldn’t have to handle them explicitly.
"I see that FixupRedirectedAssetPath is used reasonably extensively in the Engine at runtime in other locations, like World Parition for example, are those usages incorrect as well?"
FixupRedirectedAssetPath checks both CoreRedirects and the UObjectRedirector list maintained by the asset registry. In the beginning of UE4 only manual UObjectRedirector lookup worked fully, so some of those cases that you see are there for legacy reasons.