Sorry to necro this thread, but it still may contain relevant information for myself and others, so here I go:
So I finally stumbled upon the Processor Affinity setting I originally asked about in this thread (-set_cpu_affinity) listed under Troubleshooting in the Knossos launcher. Unfortunately, it requires an additional value which the wiki doesn't explain clearly. Also, if selected under Troubleshooting, it places the flag in the "Full Command Line" area of the FSO Settings box where you are unable to edit - and thus you cannot add a value behind the flag even if you wanted to.
Trying to "trick" the launcher by adding the -set_cpu_affinity flag to the custom flags area ends up with it being stripped from the custom area and added back into the Full Command Line area after hitting the save button (Knossos is a little too smart for its own good sometimes).
As far as the optional values go, I'm guessing it will follow the typical Windows Affinity value scheme of 0-3 on a 4 core processor (without Hyper-Threading). Perhaps additional values may be needed if HT is involved, but I'm just speculating.
Anyway, any input on how to properly use this flag in Knossos would be appreciated.