Every fret leveling tutorial I’ve come across says to ensure the neck is straight before filing and they say to use a notched straightedge to do this.
I will grant that you want a straight neck before filing, but only up to a point. I think the intent of this directive is to make sure the neck is returned to "neutral", or no longer under the same truss rod load that it had when it was attached and strung up to tension. A "shorthand," if you will, for "Slacken and remove the strings, then remove the neck (if a bolt-on.) At this point, the neck will likely have some strong backbow, because the rod has been tensioned to counteract the now-absent string pull. So adjust (loosen) the truss rod so that you are back to working with flat (i.e. not backbowed) neck." I would not take this to mean that you should focus on getting the
board perfectly flat at the expense of focusing on the goal of level
frets. This is where the notched straightedge advice does a disservice.
Consider the example of the scalloped fretboard:
Scalloped Fretboard | Seymour Duncan. What useful information would a notched straightedge provide you in fret leveling one of these?
When I was learning this stuff the first time, I found advice from both camps: "use a notched straightedge to check for a level board" vs "use a straightedge across the fret tops to find your initial level point." A few minutes of thinking about it abstractly and several years of practical work have both put me firmly in the latter camp. But...this is all about finding "flat," and that's also not exactly how I approach it...
Rather, I pretty much follow Bruce's approach
outlined here, which is framed primarily around having the truss rod engaged at a moderate load. Ideally at that point, the frets will be "mostly flat" already as a result of being a) all the same height and b) installed in a known-flat board (as Bruce puts it, "With the truss rod partially tightened like this, the fingerboard and frets should be pretty close to flat, because I also cut the radius on the fingerboard with the truss rod partially tightened.") Not totally, though, if loading the rod a bit also induces a bit of backbow (for one thing, filling all the once-empty slots on a level board with fret tangs in the interim step of installing frets will have an effect).
So the goal is to start with the truss rod partially tightened, and the hope/expectation is that this will have the
effect of bringing the
frets (forget about the board at this point) mostly flat. But "mostly flat" is a second-order effect of all the work done so far -- not the goal: The final fret leveling work is what will get you to "totally flat." I usually have the slightest bit of backbow at this point with a newly-built neck, but that backbow is well within the tolerances that fret leveling will address. From this point I spend maybe 10 minutes total going through the 150-, 180-, and 220-grit sides of my leveling beam. After the sharpie marks are gone, I verify with a straightedge (again, fret tops are the concern here, not the board), double-check with a rocker, then move on to polishing.
With an older neck (i.e. not a fresh build), you'll probably want to determine a "flat" state as being the point, if you can find it, where the truss rod still has plenty of room for adjustment and the frets are as close as possible to flat relative to each other (again, fret tops, not the board.) Your task here is to re-establish this flat plane across the fret tops to address any variations from the mean that have come about over the years, while only removing the minimally necessary amount of metal. If you can find this starting point - truss rod still functional and fret tops flat, then the relative flatness of the board should not be a big concern. If you can't find this starting point, then the board might be part of the problem and it might be time to pull the frets, re-level the board, and refret - but that depends on the situation.
