I think the "threat-radar identification and location system" is used to find targets for the AGM-45 Shrike missile. It's not IFF.
After more digging I can confirm you are correct on the bent probe and I was wrong. NZ's A-4Ks were delivered with APG-53 radar and straight probes, so the straight probe was not an issue for the APG-53. They got the bent probes latter.
My knowledge comes from the A-4K, which is based on the A-4F, so it's probably not correct for the A-4E.