In full scale aircraft the EGT is taken right at the exhaust valve. Not all over the place there. Infrared guns do not actually measure temperature. They measure infrared heat; the temperature they give is an educated guess. If you have a powder coated black engine and white engine running at the same temperature the gun will give a higher temp for the black engine because black radiates infrared light better. Likely the black engine would actually be cooler because black radiates heat better.