The permit status of the second unit matters more than the layout itself. A legal, permitted second unit with its own egress windows and fire separation is assessed as legitimate income-producing space, while an unpermitted second kitchen or entrance may not be reflected accurately on the roll at all, which cuts both ways depending on whether you want it counted.
Two identical-looking two-family homes can carry different assessed values for this reason alone, since the assessor is working from permit records rather than a walk-through of what is actually built. Checking your property record against what is really there is worth doing before assuming the bill is wrong.
A two-family purchase or sale is really two valuations in one, and getting both units' status right changes the number more than the square footage does. Get your hand-reviewed valuation from Joel Dyck.