I wonder if the head was a deflective casting and came from the factory like that. If it was on the PS of the block originally maybe it wasn't much of an issue. But if it was swapped to the DS during the rebuild, maybe the restricted coolant flow became a problem where it wasn't before.
Either way, good thing they dyno'ed it and caught the issue. Imagine the frustration if the motor was in the car and overheated several times and a ton of money spent on radiator/fans/etc. and still no solution because who is going to look at the cylinder head to see if it is restricting coolant flow.