I'm guessing that sanding it entirely on the bass side would still reduce the size of the holes to a significant degree, but you've already mentioned that a better solution might actually be to make those holes bigger.
On balance the obvious response is that, when you're working with an expert, you're usually best off leaving it to him! Please just pretend that it's your own bass, Andy, and do what you would do if that were the case. 🙂