Honestly, I think it was you who missed his point. He doesn't mention what you said at all. Please read his post again.
His post is actually an argument for why Apple must be working on a default app system which they will release before 7.0 final. But the argument is very weak when you break it down and pretty much goes like this:
1. I think Apple are working on a default app system.
2. Their current way of deleting stock apps isn't a complete implementation of that system.
3. Therefore they must be working to complete their default app system.
But what I tried to say is that if you take away the assumption in point 1, and suggest instead that maybe Apple are simply providing a way for people who don't use stock apps to hide them, then if you judge the feature purely on that desire, this feature fulfills that desire. You don't reach the conclusion in point 3. And yes, what I've said is a bit tautological, but my point here is we can't assume what Apple are doing or planning based on this ability to delete stock apps. Removing stock apps is removing stock apps, and that's all it is, for now. Understand this and you'll realise how silly this sentence sounds: "Hiding them is all well and good, but you then cannot use them."
OK, let me rephrase my question then. Why should Apple let us hide stock apps if we cannot replace them? I have said it before and i'll say it again, the implementation is self harming because with the stock apps being hidden it removes the ability to do certain things, such as send emails via deep links or using Siri to ask for directions for example. Letting us hide stock apps and then popping up a message on the screen saying we need stock apps is an oxymoron and its baffling to me. If Apple is still working on fully implementing this system and that options to use third party apps in their place is in Apple's plans, then I can understand. But if "Removing stock apps is removing stock apps, and that's all it is" is their goal, then this I cannot understand.