I don't like it either. Plus, like just about every rule we have, we give them some extra on top of that. They should never have specified a length because you know coaches will see that and use the full 1/2 yard every time. Then when you warn, they'll say "but we're allowed 1/2 yard!". The whole article is fine except for the 1/2 yard.
Plus when centers do that, it pushes the DL back and even makes them offside. Do we use the original LOS and let the defense be 1/2 yard offside now?
The neutral zone is established when the ball is made ready for play (2-17-1), so any snapper moving the ball up doesn't change where the neutral zone is located, nor does it make the defense offside if, as a result, there's now some overlap because the snapper is holding the ball ahead of the neutral zone. By rule, that is encroachment by the snapper.
This is a fairly common issue with many snappers in the European game. Not by half a yard, but certainly enough that it's noticeable. When I used to work line of scrimmage, I'd often be telling a coach that the reason the D-line looked offside was down to his snapper moving the ball up, not the defense, then pointing out that the only foul by rule was encroachment by his snapper, and if he wanted me to throw that on his team every time his snapper picked up the ball, sure, no problem coach, we can do that. That normally resulted in said coach going quiet and quickly finding something else to worry about.
I'd also always give the defense the benefit of the doubt any time a snapper did this.