The author misunderstands some of the complaints against Apple. In this case: (1) Apple is effectively a monopoly, much more so than shopify. (2) the author can still sell to customers your SAAS service, just not through the shopify store. (3) I could be wrong but I believe the shopify store brings lots of customers. For most developers on the app store, apple does not bring customers (this is why many people argue that apple might take a higher cut for those who find your app on a chart, and a lower cut for just using the link or branded search).
If they don't believe the inbound flow is worth it, then just selling direct to customers should make sense.