Thank you for the additional info.
As a workaround could you modify UItemDefinition::UpdateAssetBundleData so that UAssetRegistryHelpers::FixupRedirectedAssetPath is called there instead?
FixupRedirectedAssetPath is a pretty slow function and ChangeBundleStateForPrimaryAssets in the AssetManager is called frequently, while UpdateAssetBundleData is only called at save and cook time.