It isn't based on the footprint of the building, it is based on the size of the lot the footprint is on. A one-story building covering an entire block gets a 1. A 2-story building covering an entire block gets a 2. A 4-story building covering half a block get also gets a 2 - for the whole block. A 2-story building covering a whole block is more dense that a 4 story building covering half a block, but using the City's method they get ranked the same. The best way to measure urban density is lot coverage and can be easily visualized using a black plan. Central Paris is one of the most dense built environments on Earth, and with rare exception, every building is less than 6 stories. If we want density (and I am not sure we actually do) we need to take height out of the equation.