Hi there. We use Photoshop CC to insert the sky, replacing the old sky, using a custom selection process etc.
I've even tried adding a perfect gradient sky via photoshop, and still, the seam generated is very visible, even though, obviously, a gradient should present no seam whatsoever. It is as if PanoTour is adding contrast each side of the 'join', a thin highlight, and a thin shadow when joining the sky or gradient at each end of the pano (when generating/building) the 360 tour.
From my own efforts to compose skies on panos i can say: it´s almost impossible to do as long as you go over the borders.
Try to do it in a way NOT manipulating close to the borders but stay in the existing surrounding and keep away from the borders.
This works fine usually.
I also tried to edit skies on the cube-faces by composing them using the very same values for color and tone-range.
Try this: make a sky which is much bigger than the stitch, put it on a layer above the stitch so that it covers the whole stitch while keeping
THE VERY SAME values for color and tonerange on ALL three sides of the equi. ONLY THEN you can avoid having visible seams.
Of course that only works having not too complicated clouds . . . but here you additionally can try to retouch in te cubefaces (but mind the borders
best and good luck, klaus