Early in the cook when the meat is cold, the disparity is the greatest. As the meat heats up, the grate and lid thermometers will approach each other.
Upshot is that if you control to a constant lid temperature reading, you will start out a little hotter while the meat is cold and then drop down as the cook proceeds. I think that is probably a Good Thing and may even be what Weber intended. Otherwise they could have put the thermometer in the mid-section.
(I'm speaking of the WSM - the same may be true of a kettle.)