Doug and Jim bolted Maria's
Doug and Jim bolted Maria's seat down like your last picture but not via the double set of scissor jack clamps but through the webbing between the frame holes.
The end cap with the holes for the headrest frame and the pre-positioned scissor jack clamps are a refinement from the first bunch of new Vendetta frames (and new Silvio frames). I think John did it because of some of the feedback from customers having problems getting the "loose" clamps in place while assembling their bikes - and at least one LBS.
I didn't think it was anything other than a bit fiddly but I can also see where the "cap" might reduce rotational or twisting torque around the axis of the frame tube - think of your shoulders and back pumping back and forth against the seat back during a hard, fast climb.
I think your seat clamp modification is superb. I've found the rest of the fit adjustments pretty easy to make during the "ride a little, tweak a little - repeat" stages but the headrest fit is actually pretty subtle and I played with it a bunch to finally get it where I like it. Your solution would make it very easy to do a lot of little fine tuning tweaks to find the sweet spot. Just mark the position once you find it, eh?
Your Vendetta looks good! I can tell from the settings you are taller than I am. I think the fit is just a wee bit better for taller people at the V's seat recline and headrest shape.
Enjoy.
-Eric