If I were to guess, the benefits would result from making very "tight" optimizations to e.g. networking or scheduling that are specific to the workloads they deal with regularly.

Remember, Linux is designed to run on as many machine configurations and support as many workloads as possible. To achieve this, kernel devs sometimes cannot adopt the most optimized implementation because it may lead to unforeseen corner cases.

On the other hand, a company like Alibaba knows exactly what kind of machines and workloads they are dealing with, which means that they can make those optimizations and gain a slight performance boost relative to mainline Linux.