I'll be honest, there haven't been any "benchmarks" done on this, but, in theory, when running multiple installs you lose out on the benefit of disk caching (or so I'm told). If you're running from more than one drive, then you will be creating more work as 2+ drives are trying to be read from and written to at any given time, further clogging up the I/O pipeline.
In the past, there have been discussions, on this board, about SSD vs m.2 vs solid-state raid, and now that I've personally tried them all, I can say that my opinion on the matter hasn't changed one bit: I see no performance benefit, while multiboxing, when moving from a SATAIII SSD to either an m.2 drive (PCIe), or m.2 RAID 0 (PCIe).
I have said that I should re-visit this prior conclusion now that the game has changed, so perhaps there is a benefit when playing a lot of characters, but I would still assume that the penalty for running from multiple drives/folders grows as the number of characters being played does.
The operating system controls CPU affinity, so if you've assigned all of your game clients to all of your cores, the OS is going to do what it wants—this is exactly why I set my own custom assignment in ISBoxer.
On top of that, both Broadwell-E and Skylake-X use Intel's Turbo Boost 3.0 technology, and as you say, this creates "preferred cores." From what I understand, if you have the Intel Turbo Boost Max Technology 3.0 software installed, then you may see odd core assignment, as Intel states on their FAQ: "The software user interface and driver allow users to prioritize programs by directing workloads to the fastest core first." So, if you don't want that behavior, and you have that program/driver installed, then I would remove it, but I wouldn't think that this program overrides the CPU affinity that is set, in the Task Manager, for any given executable.
Now, I will also add that you do want your active processes on the thread(s) that are boosting to the highest GHz so that you can get the most performance out of them. So, I'm not entirely sure if what you've shown in the Task Manager is such a bad thing, after all, unless you know that it's actually hurting your performance.
Personally, I uninstalled that program/driver, as was recommended to do so before overclocking, and have not seen any odd core assignment other than what I dictate, but, to be fair, I am also not on SL-X (but, again, the CPU itself does not control this).
On the other hand, my gripe with Intel, currently, is for the seemingly rushed launch of X299, the shady anti-AMD propaganda, and for the lack of solder under the IHS of SL-X.
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