As far as my understanding goes, the intention of alkali treatment is to remove non-cellulosic hemicellulose, lignin, wax and other impurities and enhance the surface roughness and crystallinity. The molecular chains of cellulose rearrange themselves into closely packed long chain, thereby increasing the crystallinity. When non-cellulosic components that seal the gap between the microfibrils are removed the surface roughness increase.
However, when non-cellulosic components like hemicellulose and wax are removed, that exposes more hydrophilic cellulose to water. Also, lignin is hydrophobic, when it is removed all we have a hydrophilic cellulose.