Kingslayer,
The problem with external measurements is not only accuracy; it is that a measurement downstream from a heat source in a secondary heat path will always exhibit compressive errors.
Using my wood burning stove example from above, when the inside of the stove is 500F, a thermistor attached to the outside wall may read only 250F. Raise the temperature inside the stove 100F to 600F and the thermistor measurement will only go up 20F to 25F.
If you could accurately measure the actual internal temperature of the CPU core in this way, then you could measure the temperature inside an oven by touching a thermocouple to the front of the door, you could measure the temperature inside a house by touching a thermocouple to the outside of a window or door, and you could measure the temperature of coffee in a cup by touching a thermocouple to the outside of the cup.
In any of these cases, the thermocouple is measuring the temperature down stream from the heat source in a secondary heat path. Raise the temperature of the oven, house or coffee 20F and you will only measure a change of 5F to 7F. Thermocouples touching the side of a CPU core are subject to exactly the same type of error. The temperature change compression is a natural phenomenon of secondary flow path when there is "both" heat flow and thermal resistance from the heat source to the measurement point. This is the normal/natural case and cannot be avoided.
You also have to remember when making temperature measurements, that a thermocouple or thermistor does not measure the temperature of what it is touching, it measures the temperature of itself. In this particular test, when 5% of the thermocouple area is touching the side of the core and 95% is touching either the ceramic of the chip or the air between the chip and the heatsink, then the temperature of the thermocouple will be an average of the side of the core, the top of the ceramic and the air temperature.
Nevin