The -135 doesn't fly in an out of trim state. When we have an A/P disconnect the jet is trimmed and will continue doing whatever it was before for the most part. 99% of the time the receiver won't even know our A/P just clicked off. Up front we can generally tell how fast the receiver is closing in just by paying attention to the trim wheel moving due to the receivers bow wave.
I wasn't on that jet though, so it's hard to tell if it was an A/P issue. I'm betting you think the boom floated up because the tanker had a sudden pitch down. I'm willing to bet it was the boom operator doing his job and flying the boom out of the way. Tough call. The receiver definitely hit the upper limit though.
The E-3's wing flex when he dives away means nothing other than he dives away. It doesn't tell the story if he had upward movement into the tanker or vice versa.
Regardless, NATO E-3's still scare me...but not as bad as some foreign Vipers (Dutch and Polish not included).