Agree with Swarfy, BSA etc - the machinist is right - I wouldn't risk trying to machine such a small amount. Always a risk it won't stay centre of bore and then it's oval and oversize.
Honing is the answer. Indeed, you normally bore undersize and then hone to size. Need coarse stones first as S & B suggest, finishing the last 1 to 1 1/2 thou with fine. Total about half an hour. Sounds like the machinist knows what he's doing but is unfamiliar with engine cylinders.