The times that I do not make it flush is when there is a decorative band with raised/lowered designs of various thicknesses. I usually make the blank to be the larger size and then round-over the end. But where there is a smooth band or nib end or clip end, I measure to the precise size.
If it is for general public or for friends sales, "close" can be OK, but for the high end priced pens, precision is your friend and those buyers willing to pay the higher prices will notice. As for me, it usually doesn't take more than 5 minutes extra at most to bring a blank the precision fit, so I shoot for this on all my pens as a matter of habit.