No huge issues, other than why you would want to do it , but...
Make the hole as small as you can. And get the thermistor as close to the cpu as you can (i.e flush). AMD actually recommends making an impression in the CPU core for making the best measurements - I don't suggest you try this
It may come as a surprise to some, but right at the CPU/HS interface, the temperature gradient may be 2 degrees C (or more) per millimeter (in copper).
To a lesser degree, the position of the thermistor relative to the center of the core is significant. But since I have no accurate information as to relative heat dissipation over the core, one spot seems as good as any to me.
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