3 thou I wouldn't worry about, most guys probably couldn't measure a port to that accuracy, I can but I modified a digital caliper to do it nearly 20 years ago when I started porting engines. Now 20 thou (1/2 mm) that would make a difference.
If it had never been touched then .003 won't make a difference. That is the max most good shops will go. Other problems show up if they go more than that like the stator plate won't fit any more on Polaris.