the argument that the article brings forward is that flat design is harder to figure out because it lacks some of the real-world metaphors we associate with interaction ("things that look raised can be pushed down", "things that have depth can be filled")

has there been research done on whether these difficulties occur in all age groups? Because I can easily see this being an artifact of tradition.

People who don't use a lot of analog devices may be confused by a skeuomorphic interface, and may appreciate the simplicity of a flat design.

You are making the "digital natives don't need the crutch of physicality" argument.

Here's what tobiasandtobias had to say about that in their blog:

Even 'digital natives' live in the physical world. We start learning how it works before we ever touch a computer, and even the most dedicated nerd spends more time interacting with physical objects than with digital interfaces. It doesn't take additional learning to know that an object casting a shadow on another is in front of that other, for example. Failing to leverage that existing knowledge is tantamount to shutting down whole swathes of users' brains.

(The blog is no longer online unfortunately.)