I'll say it again:
The practical reason why we Luthiers leave the zero fret/nut a little bit higher is because it works. Years of experience. I've built and set up hundreds of basses with zero frets. I tried cutting them level, and had too many problems. And yes, I know how to set the relief and action correctly.
The technical reason why this extra height is needed is because, when you loosen the truss rod, the neck doesn't go into the exact theoretical curve that's needed for string clearance. Its curvature is imperfect. The part of the neck around the nut and the first fret is stiffer than the middle of the neck, because of the volute on the back as it transitions to the headstock. So it doesn't bend into the perfect curve. If you measure the actual relief curve of a neck carefully, you'll find that there's a flat spot in the curve around the 1st-2nd fret area. Along that desired clearance curve, the 1st and sometimes 2nd fret are effectively high, in relation to a equal-height zero fret. Raising the zero fret/nut compensates for that. It corrects the curve. So, the first zone of the relief curve is mechanically built into the neck, regardless of how the truss rod is set.
When you press the string down at the first fret, then you are moving down past the flat spot into the real relief curve, where the neck actually begins to curve. So, there's clearance over the 2nd fret, and no buzz. Same on down the neck. The problem zone is that first fret buzzing when you play the string open.
If you cut the zero fret level with the other frets down the neck, you'd have to slightly lower the first fret to keep it from buzzing. It's more practical to take the relief out of the neck, level all the frets except for the zero fret, and then trim the zero fret to be slightly higher.
Thanks Bruce for chiming in.
That is exactly what I have experienced (not as many basses yet though