When I use external edit feature to hide seams on my textures I get some really weird noise on the edges of the fragment, which covers the seam part (the way I do it in Photoshop is to create a new layer on top of the screenshot, draw fragment covering seam, delete the screenshot layer so I only have this fragment with transparent background, save it and then apply it back in Blender). For better explanation I attached 2 images where the first one is before external edit and the second is after. I used this feature in the past and as far as I remember it worked fine. Hope any of this makes sense. Version of Blender is 2.78a with Blender Render engine.