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My old 6.9 that I turbo'ed with the Banks Sidewinder kit had the probe there. The gauge and probe was calibrated to work in that location.
Ideally you want to know the temperature of the combustion chamber. This is where it is the hottest and can melt piston tops or scorch glands if it gets too hot. For that reason with a generic probe I like to measure as close to the exhaust valve as possible. It's the hottest immediate accurate reading.
Has anyone experienced cracking of the manifold after drilling & tapping it? I noticed on the EBP probe that there is a boss cast into the manifold.
I have never. It's a round hole so it wouldn't promote cracks. I believe the boss for the EBP tube fitting provides a flat spot for machining purposes when milling.