Let's say I have a coin made by Casascius in perfect condition, and I have a second coin just made after the first one but it has a scratch on it. Then you would say the second coin is less valuable because of the scratch. But now I have a coin with exactly 1BTC, and the second is 1.0000001BTC (or something). Would you say the one with 1 BTC is more valuable or the other with the extra mBTC?
I don't think that anyone that knows how bitcoin works would mind there being a satoshi or two added to his/her Casascius coin. I wouldn't for sure. I would even consider "tainting" mine if I had any.