I think people are telling you to bring the belt to the flagship stores, not because they have special equipment, but more because a skilled craftsman is working there. I don’t have any experience regarding punching a hole on a Hermes belt, but I do have experience with a craftsman punching extra holes on my Jysphere shoulder strap. While on a trip to NYC, I brought my bag along with the strap to the Madison flagship store. They have a craftsperson on call everyday, and I had him take a look at my bag. He said it would be a simple quick job and took it to the back. When he came back, the extra holes that he punched looked exactly like the original holes on the strap and they were spaced out evenly. If you didn’t know that there were not supposed to be that many holes on the strap, you wouldn’t even know it was altered. It was done on the same day and they want me to try on the bag with the newly punched holes to make sure I was happy with the result.
In a regular boutique, at best they will need to send your item to a flagship store to be altered by a craftsperson anyway, but that means you will need to wait for the item to be transferred back and forth. At worst, a random sales person may try to punch the holes themselves and do a bad job and mess up your belt.