Set back Penthouse renovation

I am interested in knowing anyone's experience with gut renovations of set-back penthouses in NYC. Specifically, will the wet over dry rule apply if in theory, things don't line-up? It is a small 1BR and there is no way either the existing bathroom or kitchen meet any sort of building codes-small clearances and passageways. I want to relocate the kitchen to put in an area of the apt that will allow for a square kitchen that will be somewhat larger and certainly make code. I'm also interested in installing a W/D in a closet adjacent to the master bath. Again...the kitchen and bath are not likely to line-up to begin with and hope to make the case that in my renovation I will bring to code. Any experience with this?