Don't forget to protect any contact points with tape first.Over a short time,even tiny movements can rub the life out of a frame .
Yes, do this (not at the point it's bolted, but if they contact the underside of the fork crown or the seatstays it's worth spending a few minutes protecting them as you would against cable rub).
Glad the shop is talking sense. I was very confused about why they'd want to drill a different sized hole there!