There's a "fly in the ointment" of the reasoning behind this thread, somewhere. I can't pin it down, but my gut is telling me so.
Let me see if I can put this into words...
We are challenged with getting the heat out of the core. The majority of the heat gets out of the core (hopefully) via the contact it has with the heatsink baseplate. Obviously, the core is also in contact with the ceramic carrier it is embedded in. Therefore, some of the heat generated by the core will migrate into the ceramic carrier if that carrier is cooler than the core. So, the ceramic is in parallel with the heatsink baseplate as a thermal conductor. It has greater resistance to heat flow (hopefully) than the baseplate, so less heat flows through it in a given amount of time. Any path that helps, no matter how little, with getting the heat out of the core, is a good thing. Here it comes ;D
So, why is it so bad if the ceramic carrier is cooler with one HSF than another. I'm not talking about the impact that its temp has on measurement, but rather on performance. Personally, I'll take any help I can get, removing heat from the core.
If the ThermoEngine, because of its tapered base, cools the ceramic more than a wide base, so much the better. Somehow, I doubt the cooling effect on the ceramic is compromising the in-socket thermistor that much. I'm assuming you don't just have the thermistor contacting the ceramic off-center, as it comes with the board, but bent to make contact with the ceramic dead-center under the core.
Except during transition from cold to hot, or hot to cold, I find my in-socket thermistor to be within .5C of the reading I get from my drilled HSF base with a thermocouple sitting directly on top of the core. And, that is with a veritable hurricane of airflow going on inside my case. sure, there is a response delay, but once the core temp has stabilized, they are very close in readings.
And another thing! (ala John Madden) I would be more concerned about the impact the HSF baseplate has upon a drilled and embedded thermocouple. In HSFs, with good heat spreading characteristics like the MC-462A with its 3/8 inch thick copper slab. With the thermocouple surrounded by that copper, as well as in contact with the top of the core. That copper has to be wicking away some of the heat which is registering in the thermocouple junction. A junction that I might mention, should not be soldered, but welded, to avoid having the lead/tin junction interacting with the dissimilar metals.
Now, where's my 4-legged turkey...
Hoot