The answer is that yes you can but you shouldn't.
Think of it as two intersecting lines - one is the barrel and one is the scope. You want the angle between the two as small as possible hence mounting the scope as close to the barrel. If you are strictly shooting at exactly 100 metres and that is all you do (e.g. at a range) then you could probably get away with it if you zero it at 100.
This guy is gold for information;
https://www.youtube.com/watch?v=COoXVpGfXQE
He basically says you should hold your rifle with your eyes closed and let your head fall forward until your cheek is on the stock then open your eye. If your eye isn't directly in line with the scope then you need to build the stock up with a riser until it is. Otherwise you will unnaturally move your head into the correct position when shooting. It sounds like you have the opposite problem though in that your stock is too high for your scope. Have you considered a different stock?