Naturally Apple’s stores do accept Apple Pay, but it seems that the decision to accept Alipay is Apple’s way of helping to increase sales (since it uses a system that customers are already familiar with) and also potentially boost local sentiment, where it shows that Apple acknowledges and accepts Alipay.
Alipay has actually been accepted by Apple for use in its digital stores about a year or so ago, so this move seems to be a natural extension of that by allowing its use in Apple’s brick-and-mortar stores. Apple has in the past acknowledged how important the Chinese market is to them, and given the country’s vast population, there is a lot of potential to tap into.
We have also seen how Apple has given into the local government’s demands, such as removing certain apps from the iTunes App Store, although this seems to have drawn the ire of US politicians who claim that by doing so, Apple is “enabling” China’s censorship of the internet.