On the whole "Double Riders pretending to be evil for 40 years" thing, you actually answered it for yourself:
The Shocker scientist who undid their brainwashing was the grown-up Naoki (Isao Sasaki's character in the lab coat.) He couldn't have done that until a couple years prior to 2011, if not during the present of the altered timeline itself. So they were actually under evil control for at least most of that 40 year time-period since they lost and were re-captured in 1971, when he was still a kid.
(I dunno exactly how the subs phrase it, because I've only watched it raw, but that was how I interpreted it when I first saw it in theaters.)
Edit: Also, now that I've finished the whole thing: Pretty good overview. While I'm at the opposite end of the spectrum on this movie (I absolutely loved it and nearly everything about it) you did raise a lot of good points. Looking forward to future episodes!