The answer is: As you fiddle and sand the neck heal, the distance to the nut gets shorter. I also do what Sven does and make the neck longer than it theoretically measures out (my case 14th fret to the body) and then I grind away on the neck heel until the joint is square and flush to the body. In other words I give me self some extra wood to play with. A 1/4 inch or even more. If I get it right after not too much sanding, this leaves me with extra space at the nut end (a too large nut ledge). I then sand down the peghead. As the peghead thins it moves the line toward the perfect line on the neck leaving just enough for the nut. I can compensate for the thinning of the peghead by increasing the thickness of the peghead vaneer to dial in the correct peghead thickness. Also, I don't believe the 14th fret (or whatever your design calculation was) has to fall exactly at the body so a little wiggle room there. But it needs to be close because that is my reference point on where the bridge plate was placed. I want the bridge to be close to perfectly centered over the plate when I measure for final scale length (plus compensation).
I realize that this might seem confusing and my explanation as clear as mud. I am also not a real lutheir but self taught. In short, give yourself some extra wood so that you can sand away and still have a proper ledge for your nut. Dial it in by thinning your peghead or as Sven does (scandalous!) blend the headstock in by slanting it (shocking!) to hit your marks.