VAR only gets involved for encroachment if a player who entered before the PK was the player who got to the ball after the save/miss. That's what happened here.
As for the ball hitting the ref, the law states that a dropped ball should happen if the ball hitting the ref causes a change of...
The whole "we're gonna apply the laws differently here because we disagree with the interpretations" would make a lot more sense if the home nations didn't have 4 of the 8 votes on the board that makes the laws in the first place.
If you really have nothing better to do, IFAB produced a presentation with all the law changes and video examples to go with them.
The handling section in law 12 is probably the most useful. It goes line by line through the new law and gives plenty of examples...
For example, you'll never see the American flag written on at a stadium like you see with the England flag (and other countries). That one would really get a widespread negative reaction. But like you said, bizarre cultural rules.
This is straight from IFAB's presentation on the new LOTG.
And this is the image from the Brazil match.
And here's the LOTG text -
"...it is not usually an offence if the ball touches a player’s hand/arm:
• when a player falls and the...