Vulcan autopilot 'modes' indeed! It had a single Smiths autopilot with very basic functionality! I never flew it in the AAR role, but when prodding against it with the F-4 it was a nice, stable platform and was much nicer than the Victor to prod against.
The VC10K autopilot system was a little more advanced, but as with the Vulcan, thrust had to be controlled manually (except during Auto ILS).
For AAR, both pilots were required to be properly strapped-in and the flying pilot had control of the control column and throttles. One of the primary responsibilites of the other pilot was to look out on his/her side of the aircraft.
I doubt very much whether Voyager is operated in the AAR role without both pilots being properly strapped in during any close formation work.
OAP, the TriStar couldn't have continued in service for very much longer, given the increasing cost of maintaining such an elderly aeroplane. Moreover, the Mk 17HDUs were very long in the tooth. However, I do think that the aircraft was retired prematurely - I saw one in the distance over Brize at 13:18 today, so I guess that was one of the last flights of the old beast? Even though the cause of the Voyager plummet has been proved to be an unique event and notwithstanding the excellence of the aircraft in the basic air transport role, it still hasn't met its AAR spec., by all accounts.