The main reason for the lack of regularity (other than my distaste for grids and the weird notion of having the city's final shape resemble a murex shell) is that the city is quite old and grew in an unplanned fashion with new pilings being driven into the estuary floor as needed. Certainly the marine topography would have influenced things as there are a number of submerged reefs, shifting sandbars, depth changes, and channels in the area (indeed that was part of the historic reason for the selection of the site).

As to the artificiality of the construction itself, a lot of that has to do with the history and philosophy of the city builders. Land, to them, is not capable of being owned as it is not the product of artifice or craft. One can own a house, but not the land on which it stands and so forth. By essentially constructing their whole city, it can be viewed more as a collection of ownable buildings rather than a tract of land. No doubt counter arguments have been raised concerning the estuary floor, the reefs, and so on which exist below the foundations (probably there is a long history of deeply confusing legal battles to be considered here).