The Buzz Feiten method of tuning involves changing the nut and I believe replacing some frets with staggered frets (not straight).

There's a good method of tuning provided by the Guild of American Luthiers that shows step-by-step how to tune a guitar so that notes sound the same (and in tune) in different positions.

Here's the link.

You may want to use this method on your new guitar, after it's been all set-up and has settled to the conditions in your house. I used to use this method, but it became too time-consuming and I stopped caring about whether I was 1.5 cent out of tune.