It's the same warped thought process as polished frames ! Most think you've binned it and had it polished to get the scratches out or something !
Be different. You'll enjoy it and shouldn't worry about the bike being worth a bit less. It's a worthwhile price !
Paint a bike / rebuild the bike... dont matter if i went to buy a bike i know if something was not right or if it had been down the road!!!
the only time you cant tell is if who ever rebuilds it throws loadsa dosh on it to get it sparkling?
But on average that costs more than the bike is worth, the guy who rebuilds is looking for a quick sale so he wont take notice of the finer points and contrate on the main like paint, pegs, bar end etc so there will always be the small detail and if you no what to look for then you can spot a messed bike a mile away.
But the way i am is idont like to see bikes the same, i mean i like to see them personel to the owner.
so in response to all make it your own... hell you bought it for that reason