Sorry, but a ball put into the net with a hand regardless of intention will never be allowed if the ref sees it. It never has been and never will be allowed. Hence the reason Neymar tried to claim to the ref that the ball hit his shoulder and not his hand.
The rule states what it does, but Neymar's hand was in the air, out from his body, in direct path of the ball. his hand was in a position to cause a hand ball.
The vast majority of handball penalties aren't intentional or deliberate. A player gets unlucky with having their arm extended. It's almost never that they intentionally move it toward the ball.
So either that rule you posted is incomplete or the referees never actually follow it, because their are very very few actually deliberate handballs
And Neymar's handball goal completely fits into the arm extended from the body, changing the flight of the ball to cause it to score. That's always been whistled and always will be.