Yes, flat would be much easier! The fretting jig I built whilst doing a fair job of keeping everything square and locked down unfortunately obscures vision of the cut depth. I have a depth stop for the fretting saw that I use, but it can't be used as it would foul on my vertical squaring bar. I was contemplating re-doing that squaring arrangement but I have more important things to do like sanding. And sanding.
How are you measuring out? I started my test with a vernier caliper, but ran out of caliper at the 5th fret. I have some at work that are sufficient to do the whole board but even second hand these are reasonably high cost.
I've used the taped down paper template method as well but that also has pitfalls.