Alkaline stop baths generally work by either oxidation of developing agents or inactivation of developing agents or by being able to "poison" the silver grains by means of a powerful restrainer. There are other methods to be sure, but these lead the pack so to speak. The first two can stain film or paper and the latter method can make the grains harder to fix. So, there are disadvantages to all of them IMHO. I have designed a few myself and even though they worked, I have been rather unhappy with all of them.