That is irrelevant. Jefferson won the popular vote, so neither the electoral college or 3/5 clause changed the final outcome. So arguing it that they benefited the southern candidates over popular elections is wrong.The professor didn't mention the popular vote.
He does seem to be wrong about the Southerner losing every time, but there was one election at least where the 3/5 ratio gave it to the Virginian, when otherwise it would have gone to the Federalist.
For example: In 1800 Jefferson got 73 electoral votes, and Adams 65.
If the slaves hadn't been counted as 3/5s, Jefferson would have gotten 60 electoral votes, and Adams 63.
Since the popular vote doesn't change regardless if slaves are counted or not (they obviously don't vote), we can deduce that Jefferson won by a big margin in the south, and Adams by a much smaller margin in the north.