Need of refining aluminium and Hoope vs Hall–Héroult processes
I think the difference is due to the way eddy currents form Magnetohydrodynamics.

As the current flows through the conductive liquid, a magnetic field is produced. This in turn causes the liquid to be pushed (at right angles to the current and field).

In one version of the cell, this current causes stirring of the aluminum, alumina, flux mix. This is more efficient from a time and electrical point of view. The trade-off however is that some of the impurities which would otherwise get captured in the slag (waste), end up mixed into the final product.

Edit: Thinking about it some more, the reason for the mixing may be due to where the $\ce{CO2}$ gas is formed. ($\ce{Al2O3 + C_{electrode} -&gt; Al +CO2}$) Bubbles formed a the bottom of the cell would rise up and cause more stirring than if they formed near the top of the cell.