But the Matias Ergo Pro does NOT have a thumb cluster at all
Yeah, and not everyone needs thumb clusters (esp. too far out) or wants to get used a completely new physical layout. That option didn't exist a few years back, but it does not.
I believe that those who still want an ErgoDox in 2016 do want a thumb cluster, and a completely new physical layout is ok with them too. That obviously does not cover everyone, just those who want an ErgoDox now. As for the thumb clusters, I'm ok with them. Not perfect, but I can reach the two big buttons effortlessly, and the rest I use rarely enough that a bit of hand movement to reach them is fine.
the Kinesis isn't split, so they're very far from being viable alternatives
Kinesis Freestyle is completely split, and a version with Cherry MX might pop up eventually;
So a split, mechanical Kinesis is not available as of this writing. The Freestyle also lacks the wells, and as such, quickly looses its appeal for me.
Kinesis Advantage provides hand separation too, although it's fixed at average shoulder width—one size doesn't fit all, but OTOH the single-piece design is much more convenient in other ways (no dealing with interconnection, typing on the lap, moving around)… the IBM M15's and keyboard.io M01's ability to bind both halves into one piece is very nice.
I'm not going to use a keyboard I can't split. My mouse is in the middle, and it will stay there. A split keyboard also allows me to type one-handed, and mouse with the other. It allows me to position the halves in any way I want: I can put one further away, if I happen to sit partially with my side to the table, which happens when I talk to people, and still want to type (to take notes, for example), without looking at the screen. With a non-split, that's considerably harder to do.
So, in short, there are cases where the ErgoDox, even today, in 2016, has no viable alternatives readily avaliable, and thus its appeal remains. Is it for everyone? Hell no. But there are cases where you have nothing better. Granted, you could always do a custom, but I don't have the skills, the time, the tools, the motivation, or the will to do that, nor do I have the energy to find and pay someone twice the money I paid for my ErgoDox EZ, to build me something marginally better, without warranty.
The ErgoDox's appeal is that it ticks enough boxes on my checklist to be worth it, and is readily available. It doesn't have to be perfect to be appealing. It just has to be better than any of the alternatives, for a specific person and their use-cases.