Forgive me, dave, for trashing some of the fairy tales you just posted :
Generally up till now I have very few differences in lens AFFTs between the two cameras.
U-hum. That makes me even more curious, why the lens works well with one and shitty with the other body?
Sigma has to reverse engineer their AF algorithms as best they can, that IMHO plays a large role......for instance the lens information that identifies the lens itself is incomplete.....many memorized AFFT settings are confused between themselves,
It still doesn't explain the different quality of cooperation between your two camera bodies. Also, this reverse engineering often is used to point out how bad a lens will be because it's not "the real thing". But if they do reverse engineering for decades, don't you think they know sometimes more about Nikon lenses than most managers, designers and users do? And don't you see the chance that the reverse engineerers are perfectly able to avoid some flaws? I remember very well a damaged focus drive of the 85/1.4 G or the uneven working VR of the pretty expensive 300/4 PF E. None of my Nikkors ever gets a better VR result than Sigma's OS - and Tamron's also working very well. Genuine lenses are in no way any guarantee for flaw-free products, just saying.
As far as I know all Nikon's lens identify themselves independantly.
As far as you know - that's the same as I know, too, so until one tells the opposite, we can agree on that.
The Sigma 24-105/4 Art is always confused with the Micro Nikkor 105/2.8. The latter wins in the register of AFMA- but until I mount it, the cameras (this is ongoing since D800... and Sigma didn't fix it with a firmware update) recognizes a 24-105/4 lens! You know how I work around? Super simple. I use the dock to adjust the Sigma to the same +7 or so. Earlier I used paper labels with the AFMA value on them sticked to the inner side of the front cap, works also. These two lenses have very different purposes, so it's simply no problem just a bit of an inconvenience.
None of the third party lenses use the full features of the later Nikon AF system ....even many of the older Nikon lenses do not either, Nikon publish a list of lenses that "do" use the full facilities available.....when I find it again I will post it.
That statement stands a bit lonesome without some evidence backup. Which magic AF features are not supported? One would be enough. Remember, the new feature "focus stacking" or "AF adjustment in camera" (D500 / D850)? None of my not genuine lenses made any problem with using these functions. So once again: Maybe reverse engineered, but with some skills... And they don't have to reverse engineer only Nikon, but also Canon (or do they have a license to use their AF-techniques?). So, Sigma users could get the best out of two systems as originals. I don't see that as bad as you apparently do.
Between the lens identification codes and the fact that Nikon will not licence their software to Sigma or Tamron for that matter puts them to a disadvantage, as to how much that affects things in the end is another question!
No, it doesn't. Either you have "competing" lenses which head towards the same memory bank - then paper labels or adjusting one lens to the other come into play. Or one lens is identified as another - as long as it's consitent, who cares?
So enter the USB dock.......it gives us ordinary folk the opportunity to make our own settings straight on to the lens....a get round for those capricious lenses which had AF quirks here and there and giving us independence from the service departments.
In the sample before (24-105/4 or 105/2.8), the USB-dock gets me better focus reliability at all focal lengths and distances than setting one AFMA for the whole lens. It's more work, but the result is usually better than what I get out of the (fast) Nikkors.
If you don't start out with Nikon's blessing, a manufacturer is out on his own when it comes to exactly what is needed to get the job done without hiccups........and effectively Sigma and Tamron are out on their own!
... and in business since a couple of decades. If they were not good at what they do, they already went the Soligor, Tokina, Hanimex, Yashica, Minolta, Rollei path - and became unknown by youngsters.
There are many subject through the internet have been explained, exposed and been thoroughly understood, right down to the last detail, the exact working of PDAF isn't one of those!
Neitehr is the "exact" working of CDAF or dual pixel or whatever - these techniques don't work better if you can explain them exactly - you just need to learn and exercise what they do and when they are in a weak or strong zone .