Well for D1 most schools begin the seasons down south, Kids are missing school some of those games. Also I believe that D1 has an official start date. All schools start on the same day or close to it. So the west and south teams do not get such a large jump on the Northern teams. These things would never happen in D3.
Some people suggest that the spread out schedule for the West teams in D3, has been the reason that they have not won more in the CWS. They play fewer games a week so there is not a reason to develop a lot of pitchers. They usually have very good pitchers but only the top two or three have seen significant innings. Get to the regionals or the CWS and you have to win a lot of games in a short period of time. Northern schools are used to that and if they have the talent to get to the regionals or CWS, then they probably have a pretty deep pitching staff. Thus many times they are better prepared pitching wise for NCAA tournament play.