From my understanding, the issue with Jefferson was with him counting what appeared to be an illegitimate electoral vote submission from Georgia (ironic, I know) which gave him the Presidency, not that he discarded electoral votes.

With Nixon, the governor signed stating Nixon won, but a full count showed Kennedy won. Both sets of electoral votes were delivered to Washington as part of the electoral process. Nixon chose to use the "Kennedy" votes because they were the "accurate" results of the election, not the one the HI governor submitted.

Not trying to muddy the waters, but this current situation is different than the ones you mentioned, although the more recent Nixon situation is probably the better example of the two. These examples do demonstrate that the VP does have the legal authority to selectively choose which electoral votes to count.