@Alex Barr Nothing came of this in the end. The holes remain and the beams are now hidden behind ceilings. If there was a problem, I am not aware of it. You can see from the response that no one here seemed to consider it a problem that holes were made outside of the permitted zone. That was reassuring as I have great respect for the people on this forum and appreciate their time and opinions given.
But I remain perplexed as to why the builder/tradesman/overseer thinks that the guidance (or are they regulations?) doesn't need to be followed. It was not as if the holes had to out of the permitted zone for some reason. They could have easily been made within in, and it's not a very complex concept to understand. In this case, the replies here told me it was a fight that was not worth fighting.
But I can highly recommend this forum! If you have any problems/questions, then these guys (and gals?) are very helpful.