You can do it at birth, but I would recomend waiting until the foal is abotu a week old. Most foals are weak in the pasterns when they are born and need a few days to build strength and straighten out, then you can measure from the corenet band to the middle of the knee, where there is a "dip". You can do it at any age, and it should be the same assuming you were accurate. It is harder to find the middle of the knee when they are older and the growth plate closes.
AS far as deep bodied horses and shallow bodied horses, that doesn't effect their height. Tehir height is based on the withers, down through the shoulder and legs, not the rib cage/girth. The point about the shorter forearms, I'm not sure if it is true, or if it is just an optical illusion.