- if users are happy with the alt store and it becomes highly successful, Apple loses revenue it would otherwise get from its own store

- if users are unhappy with the alt store because viruses, etc., get onto their phones, or it becomes a spam-ware cesspool, Apple gets the blame (the vast majority of users will not differentiate and then Apple has to spent tons of effort to "don't buy from stores X, Y and Z"--much easier to just disallow them)

Remember, most Apple users care about an optimum experience. If they care a lot about openness they would be using Android / Linux and are not Apple's target.