They are not, tried the other way and it still causes the rocket to lose control very quickly. Did some more testing and it is only with SAS enabled. Flies straight up just fine without SAS but as soon as I turn SAS on it starts spinning and losing control. At first I thought maybe it is top heavy (which it is a bit) but it doesn't explain why it loses control as soon as I turn SAS on. Tried removing all control surfaces and fins just in case but still ended up with the same result. The only thing that worked was removing the whole top section past the fairing base and the fairing itself, then it would stop losing control when SAS is turned on. So I double checked everything in that section which was the Nose Cone, 4 battery packs, 2 antennas, 2 service bays, top filled with science instruments and Kerbal Engineering System part, bottom filled with more science instruments, Science Jr in the middle between the bays, followed by Thor X400 fuel tank and 48-7S Spark engine. Too my knowledge (which isn't much lol, new-ish at KSP) none of that would seem to mess with the guidance unit this much or at all? The guidance unit itself is clipped inside the Thor Upper Stage fuel tank, directly below the fairing base.
Here is the rocket in question:
