This rule only applies when the batter is in front of the batter's box, like the slap hitter who goes beyond the top line of the box when she gets hit by the pitch.

It does not apply when the batter has her foot completely out of the box (and/or touching the plate) when hit. For example, a batter who squares to bunt and has her back foot on top of the plate gets hit in the arm as she tries to pull her bat back on a high-n-tight pitch.

I assume the ruling in all codes there is a routine HBP, correct?

I could have sworn that I read somewhere that the onus is no longer on the pitcher if the batter has moved out of the box and closer to the pitcher and has been HBP. Forgive me if I'm wrong, but it goes with the logic that the onus is on the pitcher to not have a pitch enter the batter's box; similarly the onus is on the batter if they are going to be in front and outside the batter's box to avoid the pitch or it would simply be dead ball - ball.

Though, I'm more than happy not reading too much into it and simply ruling HBP.