And I like your approach, though for myself I would choose less that .010", but that's in good part because of how I play.
I think we measure it a little bit differently, too. You use a straightedge, touching the zero fret and the 3rd fret, measuring under the 1st, right? And you like about 0.003"?
I measure it with my dial indicator gauge, which rests a straight bar on frets 1-4. It measures the height of the zero fret above that line, parallel to it. I set my zero frets at 0.010" using that measurement. If I then measure it using your method, I get around 0.003-0.004" at the 1st. We're getting about the same final result, but measuring it differently in the process.