There are a lot of variables in a question like this so it is not possible to accurately judge the actions of the engineer that you refer to. However, we can discuss general cases.
Case 1: Assume that the diameter of the puncture is greater than the diameter of the meggar probe. You insert the meggar probe into the puncture until you hit the bottom. The meggar will accurately measure the insulation resistance of the remaining insulation or, if the puncture is complete, the probe will contact the conductor and the meggar will show zero insulation resistance.
Case 2: Assume that the diameter of the puncture is smaller than the diameter of the meggar probe. You place the probe over the puncture site. The meggar will measure the insulation resistance of the air that occupies the puncture cavity. If the resistance of the air gap is sufficiently large, you may not detect the puncture nor be able to determine if it completely penetrates the insulation.
A better method would be to immerse the wire in an insulated (plastic) bucket of water with the ends of the wire outside of the water. Place one meggar probe on the conductor and the other probe into the water. The water will penetrate any punctures no matter how small and will allow a measurement of the remaining insulation or, if the puncture is complete, it will contact the conductor and show zero insulation resistance. This method is similar to the method used to test high voltage gloves.