But how many more would have used them if there were an affordance?
And if we're talking about good (user interface) design, there's an element of "what if everybody did it" involved. I don't want a lot of applications hiding useful features behind invisible buttons. I think having the keys there is a fantastic idea; I just think it would be better if they were visible.
This is about people accidentally pressing keys on the wrong side of the keyboard. It makes sure that those people are not interrupted in their writing, while still presenting a clear image to the user that is not confusing. It’s a line of defense, like the buttons that are actually a bit larger than they are displayed – just in order to make sure that users missing those buttons is less likely.
It’s error correction. The feature is not that there are repeated buttons on the keyboard and users can pick which they want to use. Users are not supposed to use those. They are not supposed to know (or have to know) about them.
I'll grant that if you're optimizing for error correction, it's a perfectly suitable solution. I'd even go so far as to say that's exactly what Apple was going for when designing this. Even so, I really think this is a case where showing that this is an option would be valuable. When I see a split keyboard, I assume that I need to press the keys where they're displayed and frequently have to slow down my typing to figure out which side of the keyboard the key is on. It's nice to know I don't have to do that.
Also, I wouldn't take that initial comment as a dig, even if it was intended as one. I think it says something about the the discovery of this feature that you couldn't immediately realize the intention. The fact that it's not obvious to everyone what this is for gives even more reason for it to be a hidden feature.