I noticed this quite some time ago as well. I measured the dot placement & size from the tops of the F&R sights and they were the same so the only logical explanation is it's a combination of parallax & perceived dot size due to the distances involved. In theory, if you line up the three dots through the centers and place the front dot for the POI it should be the same as using the tops of the sights and using the top of the front sight as the POI. This assumes that the dots are all the same distance down from the tops of the F&R sights.
On all of my M&P's (9FS, 9c, 9mm Shield) I line up the tops and place the dot on the planned POI. My M&P22 shoots with a 12 o'clock sight picture even though it's got a 3-dot setup on it.
As mentioned previously, at combat distances it probably doesn't make any real world difference if you're just going for a COM hit. If you're trying to do a precision shot then it might make a small difference.