From my reading, research, product development experience and use in the field, I would say yes.
Hypo-allergenic: Alpaca is considered a dry fiber, without lanolin that is found in sheep’s wool. Some clothing lines of wool are now being promoted as “superwashed” for next-to-skin capabilities by removing the wool’s lanolin and barbs. According to Textile Chemicals: Environmental Data and Facts, the superwashed wool is treated with synthetic resins (polyamide / epichlorohydrine or polyurethane), a method that can include such chemicals as chlorine and hypochlorous acid, sulphuric acid, sodium hypochlorite, alkali metal salts of dichloroisocyanuric acid (DCCA) and an acid-stable wetting agent. The chlorination process for wool has lead to enormous environmental problems. Alpaca now offers an eco-friendly alternative to natural fiber active wear.
Almost Completely Waterproof: Yes, if you pour water on alpaca, it will get wet. However, it does offer great wicking abilities. Wool will absorb up to 50% of its body weight in moisture, but after this there is a saturation point and the sweat can sit next to skin, increasing discomfort and likelihood of blisters (socks rubbing against the skin). Because alpaca is hollow, it traps in more heat and mechanically pushes the water away, never having a saturation point on the skin. Essentially, the water evaporates because of the warmth of the alpaca.
So the answer to my initial question, is there really a difference? Definitely.