The re centering happens in normal vr mode, and is working as intended (in that mode). The elements recenter before shooting. The lens looks perfectly sharp, even with a tc. His comments in the video are varied but... Based on his images, I don't think it's a huge difference. It also looked like his exposure was slightly different, among other things.
Obviously a lens is likely to get some amount sharper as you stop down, but I'm not sure the difference is actually that much here.
I also don't agree with your comment about the eye detect range. I've found it did as good of a job (give or take, it was in the field, not a scientific test) as the a1, and I've heard it's as good as the r3 (again, like give or take, but close enough at worst) from people with that (I haven't spent enough time with one myself, though I have played with one).
Using 3d is also not the mode I'd use, but duade is used to that. Wide area with SD is my starting mode, with buttons set up to change that depending on circumstances. This is more in reference to his prior video.
That all said, I like his videos and he's very good about being fair about what's he's saying. I also really like how he shows his images (shows the raw, and then his edit with the crop).