I think the reason for placing scrim on the backing side is because quilts are normally quilted from the top. If scrim is on the top, the needle could theoretically punch the batting through the backing creating little "beards". In reality, I don't think this is likely to happen with modern batts because of the manufacturing process. Needlepunching means that fibers are much less likely to beard.
Also, if you think about it, the manufacturing process of needlepunching through scrim (which is how Warm and Natural is made) means that the fibers are on top and the scrim is on the bottom during the needlepunching process. Placing the scrim next to the batting simply reproduces the manufacturing process -- instead of working in the opposite direction.