I think the issue here is Waterdeep has not been portrayed consistently over the years. Since it's pretty much the oldest continuously occupied city in D&D, that's probably not surprising. In particular, the artwork portrays it as steep and rugged, but maps often flatten it out. I think it's mostly a case of it being easier to draw maps if you make it flatter. In another thread I commented on a model of the Roman settlement of Deva, which made it pretty much flat and at water level. Something that I know, being familiar with the modern city of Chester, simply is not true. It's a cartographer's fiction.
Generally, if your issue is with Waterdeep being flat and at sea level, I would say that the correct conclusion to draw is your map is wrong, not that the city is wrong.
Oh, and BTW, my first job was "Trainee Cartographer"!