I could be completely wrong here but I thought the bore size was only the diameter of the piston and had nothing to do with the height. I wouldn't think the head would matter as long as the piston wasn't taller. I know that I have had to go up in bore sizes and the head was never touched. No problems here either. Does this shop normally work on bicycles or something.
Like I said though, it's possible I have no idea what I'm talking about.