Yes, you are perfectly right alQ. But I have to say this, it's a bit Intel's fault for this confusion: they have a technology that makes each physical core behave as two virtual/logical cores and call it Hyper
threading even though it has little to do with actual programming threads, and on their CPU database they explain a CPU with HT by saying it has, for example, 2 cores and 4 threads or 4 cores and 8 threads, and so on, and that is why I always end up saying threads when what I actually mean is virtual/logical cores, which is they way they are called in the Task Manager, for example.
So from here on I'll say a CPU with HT has X physical cores that work as 2X virtual/logical ones, so we can avoid all this confusion.
Oh, and by checking my CPU-Z report I've found that logical cores 0 and 1 are both on physical core 0, and logical cores 2 and 3 are both on physical core 1, etc., when HT is enabled, which would explain the bad performance if, in a HT CPU with 4 physical cores, TW just starts loading (logical) core 0, then 1, then 2, then 3, because it would actually end up using 2 physical cores instead of 4! Luckily your settings tweak seems to solve this in some way.

I think they might have done it for how the Turbo works: the Turbo speed applies to the physical cores only, so if you use only one physical core the CPU uses the highest Turbo value, with two physical cores it uses a little less, etc. so by using the least possible number of physical cores they make the CPU use the highest Turbo values. Which is utterly stupid, because using two actually physical cores at 2.3GHz instead of two logical cores on the same physical core at 2.4GHz, is probably faster.

then you have nothing to be afraid of, you have sooooo much thermal headroom, just look up your CPU maximum safe temperatures and stay within them. You could easily reach 4GHz without even coming close to overheating it, if the CPU takes that speed!
And yes, the CPU, no matter how powerful, always ends up bottlenecking the GPU in TW, unless your GPU is veeery crappy and extremely old, but yours, even if a bit old, is still decent, as you can tell from your fps, and it's also within the game recommended specs (even though they are pretty vague).