I think you have far to high exspectations to NKS as it is. But that has nothing to do with compatibility.
Have a look at this video: Best way to midi map Arturia Minilab Mk2 in Komplete Kontrol using Memory Slots!
https://www.youtube.com/watch?v=e1AEzW2NS_c from just before 6:00 minutes.
Then please tell me why it's a major issue to use midi learn in this context? It's done in seconds once, at that's it. After this when you change presets in Komplete Kontrol it work without using MIDI learn anymore.
It's also possible to link buttons for preset up/ down, plugins left/ right and Plugin pages back/ fourth the same way. Just link once - and then no more.
By doing this you can say, that any third party controller is compatible with NKS.
You need a NI Komplete Kontrol controller to not use MIDI learn for this, and to have more integration with the Komplete Kontrol application. But you will have to use MIDI learn for many things that's not working with Komplete Kontrol system anyway. That include DAWs buildt in applications as it is. I have in example not heard of any DAWs own synths that use NKS.
You have to use the Komplete Kontrol application to have NKS working. You have to work in NI's ecosystem and in example not use Arturias own presets and presets system, as that's two different things. NKS do not use Arturia presets, U-He presets, Tone2 presets and so on, and as such you in example don't use the excelent browser functionality from those vendors as it is.
Arturias applications presets browsers and Arturias internal preset system is poverful. That you don't use, when you use NKS.
I can suggest you watch this video: Komplete Kontrol vs Nektarine (Nektar Panorama T)
https://www.youtube.com/watch?v=mbRtT6ovfvE - Keep in mind the video is'nt completely new, so perhaps there have been slight changes. But it can help to see how things work, and i don't think there have been major changes with NKS, I have the Komplete Kontrol application btw. I can control it with my old Novation controller that btw is a automap controller that also was a system to have pre mapped presets, and it used the manufactors own presets as it just used automation patameters. Novation no longer have that system.
I don't think a perfect system that include all excist yet. I think it has to be a open system and not owned by a single vendor like NI.
To me it's vital for a good keyboard controller to be good to play. It shall in example have good velocity feel and a good aftertouch feel. And it shall have At least 9 sliders to use with a Hammond organ drawbar section. It shall also have some buttons and knobs. 9 of each or more. And there is more. Even the layout of the controller is important.
Why does Arturias controllers appeal to you?