Nice illustration of N1K development progression:
As ordered, a seaplane fighter. The "N" prefix means seaplane fighter, the following "1" mean the first such ordered, then the "K" means designed by Kawanishi and lastly the second "1" means it is the first version.
N1K1
In the next version the floats have been removed and it has been redesigned as a land based interceptor. The letter designation for land based interceptor was "J", so that is now added on as a "-J" indicating it has been modified to be a land based interceptor. You can see this code style at work with the A6M2-N "Rufe" as well, a carrier fighter "A" modified to be a seaplane fighter "-N". In the N1K1-J it still retains the mid-wing construction of its seaplane roots.
N1K1-J
In the final service version there was major redesign work done. The wing was lowered to improved pilot visibility and removed the overly complex telescoping landing gear that were prone to failure. The tail was fully redesigned. The cowl guns were omitted and all four of the 20mm cannons were moved inside the wing. The ammunition supply for the 20mm cannons was made integral to the wing, greatly increasing the quantity of ammunition that could be carried. Most importantly the total number of parts, and consequently man hours to build, were cut by approximately 50%.
N1K2-J
As to the wing roots, here is a screenshot of our new N1K2-J:

The fairings might extend a bit too far back on the new AH N1K2-J. It is hard to tell in the photo of the N1K2-J as the green color does not show depth very well in that lighting. The black and white photo of the N1K1 does have large fairings, but that is a mid-wing design from before the major redesign so I don't know how valid it is. In the photo of the N1K2-J as compared to the screen shot it seems the fairing starts further back on the wing and doesn't go quite so high up the fuselage. It is almost as though the fairing shape is the same, but the fairing polygon on the AH model hasn't been pushing quite far enough in.