Assuming that I understood your question right (which may not be the case

) making a template with a wacked-out guitar should not be a problem, except in the case where you use a really-really-really (you get the idea) messed up guitar where the scale-lenght is not accurate (and therefore the frets are not spaced as they should be).... A straight-edge will remain a straight-edge whether the neck is curved as heck or not. What you wanna do with this exercise is get an idea (rough approximation) of the frets spacing. Since you're going to make the slots wider than the actual frets (and that odie specified that you'll probably need to re-grind some of 'em) you only get an approximation, which is what we want. Of course if the neck's as curved as a bow you'd be way off but I don't think anybody would (or should) used a guitar THAT screwed-up as a template....
Second, all the notches have to do is not touch the frets, their dept doesn't matter....
Odie: Great tutorial indeed...thanks
Anybody feel free to correct me if I'm missing something (or if I am actually not reading your question right T4D

)