I think you might get different answers from different people, because I suspect there are a variety of reasons why someone might prefer this layout over another. Some might say the "Windows key" is redundant, as other key combos can do the same functionality. Some might argue that fewer keys can lead to faster work as your fingers have less of an area to cover. Some just may prefer the visual aesthetic. Personally, I was attracted to this layout for retro nostalgic reasons.
However, I think when it comes to your point of "paying a premium," the number of keys is not the sole criteria here. If Logitech were making keyboards in this layout, I'm sure they could have $30 keyboards on the shelves. But, at least as is the case is here with the Tokyo60, we're talking about a machined aluminum body and fully customizable hot swap pcb. If you wanted a larger sized keyboard in this same quality, of course you're going to pay more for it too.
The keyboard and pcb by itself with no caps or switches was $175.
That's pretty inexpensive compared to other custom aluminum keyboard kits I've gotten through Geekhack group buys, and none of those kits have hot swap pcbs. (Though they have been 60% boards or larger.)
I'll be honest with you, I wasn't sure if I'd like the small layout when I first got it - after using full sized keyboards for so long. But after some time, I've found that I really enjoy using it. Getting just the right switches and keycaps go a long way in that user experience, but the part that surprised me most was just how comfortable and natural certain keyboard shortcut combos become after awhile. And it helps a lot that you can be the person to define what they are and how they work.