The real issue it (along with the 3/5 compromise, the structure of the Senate, and the limited term explicit protection of the slave trade in the original Constitution) addressed is that, in the early US, slavery wasn't all that popular in the states that were more urbanized and had economies and value systems that supported growth in the enfranchised population, so the system had to be skewed to protect the masters in the disenfranchising states for theme to feel secure in their "peculiar institution", even if that meant sacrificing the ideal of equality even among the enfranchised citizenry.