It is not up to schools or conferences to determine punishment for NCAA tests but they are able to determine it for school administered tests. Which again is the reason schools test so they get players clean with lesser punishments before the NCAA tests them. Our first strike for weed is just probation, so its likely there are even more players on the team who have tested positive that we never even find out about. IIRC, the athletics department doesn't even tell the coach about the first violation and never tells them the specific drug if the player is suspended.
And while the NCAA might say they only test for pot at championship events, it is still in the rules that they can test at any time. So if some team lets it be known that they aren't testing for pot anymore, the NCAA could step in and test for it on that team more often.