Waterways, you're right about the footprint of a building affecting its height but this works both ways.
The Cesar Pelli building in the PDSA has lost 3 floors which, besides massively reducing a developers potential value from the site, makes the reduced finished article appear stumpy and misshapen and consequently has a far worse effect on its neighbours than the original plan would have. This factor is never taken into account by those who think they are protecting the city by introducing height restrictions.