I set my nut action by filing the slots in the nut [not the bottom.] You can individually adjust each strings height that way as well as ensure you get the correct break angle from the nut to the tuner post. [If the strings are too deep in the slots after cutting, I file down and re-shape the top of the nut to give me the right depths.]
I set mine with the string depressed at the 3rd fret. The measurements I typically aim for is .004" for E1 to G, and .008" for D to E6
(sometimes the D can go a bit lower). This is just my preferred method and what works for me.
[Tip: if you don't have feeler gauges, typical copy paper is about .004" thick. Just a 1 cm strip to slide under the depressed string. Then just fold it over (.008") for the heavier strings.]
Like with most things guitar, the numbers are not carved in stone. They're more of a reference point. Each instrument has it's own set of rules!
[edited to add more info]
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