Careful: Don't go there until you read the shop manual first! If you start 'messing' with the alignment spacer screws you should understand how they are setting the glass to glass distances for which there are specific V.W measurements and tolerances. These not only set the front to rear glass distance gap so they don't touch each other, but also the glass location in the top seal that stops water running inside next time it rains. If you move the rear glass in-out too far, contact pressure on the vertical seal increases load on the window motor and regulator and the seal will start forming a pressure indentation. The EOS window glasses are curved and correct contact with the vertical seal and gaps must be checked as the glass rises from down to fully raised.Enjoy the job
IMHO the best compromise is to get the horizontal gap distances and levels correct first to V.W spec., then only move the rear glass sufficiently inwards to get light pressure contact on the vertical seal which you can test with a smear of Krytox. This assumes the front glass alignment hasn't been messed with or not adjusted after a DIY regulator repair? The front glass alignment on both sides should be checked first before messing with the rear glass.