I don't disagree with the building complements and addons forever - no one is arguing that. I would say that the difference between building an application for one company vs building for a platform has some pretty distinct differences.
I think in this instance if you are building for large swaths of a population (ie. merchants) and the brand reputation (Shopify) is at risk of a bad actor (i.e. in Facebooks case cambridge analytics) it is in the interests of the brand (ie Shopify) to manage risk from bad actors.
This may be a cash grab, I don't know the true details only the comments from the aggrieved developer. Though reading the aggrieved comments they seem to have been playing by their own rules and got caught.
If the argument you are trying to make is upstream of that in that the layout of the internet is no longer favor of individual developers - thats a bigger debate that I don't think we can address here. It's a market structure argument in its essence.