McDave,
It's been a long time since my Basic Mechanical Skills training that I went through, but somebody can correct me if I'm wrong. There are lots of cylindrical things that the primary source of being "out of round" is at the ends, bar stock, etc. I think they call it runout or something. So I think the answer to your question is yes, cutting small amounts from each end would have a higher probability of bring something of .006 straightness closer to .003 or .001. Whether are not it is worth your effort to do so is probably 100% mental.