Yes, you are missing 'something'.
Registration, IN ANY FORM, be it ballistic 'fingerprinting' or any other such nonsense will give power to the state to track you. It also means when they 'outlaw by decree' whatever guns you have 'fingerprinted' they will just knock on your door(in lieu of kicking it in) and confiscate them. Can't happen here? Look at California, first a ban on manufacture of military style weapons, then a registration of those in state, then a total outlaw of them, 'criminal by decree'.
If stolen and used in a crime, you will be held accountable, sell it and that sale will be tracked, the cost of the system would be close to $5000 a shell casing, and guess who pays for that?
Yeah, you're missing something..... A LOT.