I take it you place the nut on the peg-head angle and not the fretboard surface. If you place the nut on the fretboard plane, you don't have this problem as the neck is roughly 3/16" longer due to the nut. I'm cutting two necks right now and have been through this as I use the Allied rods.
I've also elected to install a spline over top of the rod, it's only 3/32" but it puts the rod just a little bit lower in the neck which will not help much but every little bit counts. The Allied rods are plenty low profile enough to put them lower in the neck, just lay it all out (I'm sure you have a couple times already

) because paper and wood work so much alike

(Ya Right!)
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