Welcome back and thanks for the question. It's great to see people really breaking down the video's and paying attention to alignments. Makes my work on bringing them to the site very worthwhile.
Bear in mind that although John is one of the best ballstrikers on tour, his is a work in progress, just like every other tour player that is looking for the ideal pattern including Tiger. So it's not perfect, but getting closer every day he makes a golf stroke. Under Rob's guidance, he will be raising many championship trophies, and it could be any day now.
He is a golf athlete like nearly every player on tour, so he will get impact alignments right with some effort. The idea is to make them effortless and full of confidence. He has all the tools he needs.
These videos were taken early this year and John mentioned to me last week he is swinging even better now. Note that he is a swinger, not a hitter so don't attempt to pattern your swing (hit) after his. It's a pivot powered swing with the mind in the hands. Only Rob and Lynn can comment on the things John is working on right now, but if you look at some of Johns old swings from two years ago compared to what you see in the gallery, the alignments are light years better now.
Rob, Lynn and John can give you the details. All I can say is do what John does in concept. Model your swing (hit) based on ideal alignments found in the yellow book and practice them until you own them. Lynn and Ted are more than qualified to help you work out all the hitting details.
Please keep posting. Been missing you around here.