Hey there, not sure I follow your question. What's the difference between what you call a deck scupper and a transom scupper? When I drilled the holes for my scuppers I got them as low as I could get them based on the floor of the boat.
i think my transom scuppers are an inch lower than the deck scuppers. maybe 1-1/2 inch, i dont remember. between that and there's a good downward flow to them thanks to the drain trough they sit in, its about one of the best draining boats in my marina.