According to the description found on the front of the instruction booklet, a special version called the 9901a was developed for Pups deployed on ships at sea. Most Pups were stationed on land near the coast. The stitching in the fuselage was to access flotation bags installed to assist recovery after the aircraft was ditched in the sea next to it's tender, before the use of dedicated aircraft carriers. The window in the upper wing was commonly found on those aircraft.
There are six sets of markings for the RNAS kit. The first four do not use the differently stitched fuselage or the upper wing with the window in it. I don't know if the Pheon decals differentiate between the two types but it appears that non 9901a Pups were flown by the RNAS as well.
Hope this helps, I have an RNAS version and I just picked up a couple RFC kits. I'm pretty sure I'll be using one of the other markings from the RNAS kit for one of the new RFC kits, the cockades look the same for the non-9901a types.
Dwayne