You may find the following link to Bill Maxwell's completed Swan class build of assistance. It has 247 high definition pictures taken during Bill's build of HMS Fly.
You will see that the edge between each of the planks forming the Stuff of the Topside is flush. The sheer strake immediately above the Stuff of the Topside is proud to the plank below and above it, ie similar to the main wale. This treatment appears consistent with the text of David Antscherl's TFFM, Sections 7.17, 7.19 and 7.20, and also consistent with the photo CD accompanying the kit, eg refer photos IMG3359, 3422 and 3432.
Hope this helps,