The point is that the barrel is ever so slightly angled upwards when you fire the gun. The bullet travels upwards until it reaches its peak and then begins to travel downwards. Regardless, as soon as the bullet leaves the barrel, gravity starts working on it, and starts pulling it downwards. It is only because the barrel is angled upwards to begin with that the bullet is able to travel above the sight line until gravity finally stops that and starts it back downwards.
As such, no, the chart is not necessarily incorrect. My guess, based on the zero distance, is that the chart is based on the sight line being 2.5 inches above the center of the bore. It would be much better if they called that out specifically, though. Of course, the ballistic coefficient of the bullet also has an effect. Without knowing that, the chart is less useful than it could/should be.