Apologies for the double-post, but I've got a status update.
I've tried changing the thread count and that definitely makes a difference...but still causes issues. Having a thread count of 4 or less lower causes the poor performance issue mentioned in the first post while setting a thread count of 5 or more solves the performance problem but causes the weird flickering issue I mentioned months ago that can only be solved by (other than lowering the thread count) turning on "global refinement" or disabling GPU acceleration.
EDIT: ...and now Einstein is rolling in his grave - I closed MPC-HC and re-opened it and now the flicker issue isn't occuring. For reference this was like the third or forth time I've closed MPC-HC, and yet only now it's suddenly working...
Other than that, the only difference was that I enabled "Global refinement" and then disabled it. Maybe even just doing that fixes the weird flicker issue?
EDIT 2: *sigh* poor Einstein... now after a reboot the flicker issue is back, and changing threads and enabling global refinement isn't fixing it. Maybe I just need to keep restarting MPC-HC and eventually I'll get lucky?
EDIT 3: Yup, seems like it's just a lottery - just keep restarting MPC-HC and eventually the flicker issue won't occur (seems like ~30% chance of it working correctly). Alternatively you can just disable GPU acceleration in SVP and that'll solve it completely...