Only take 2 measurements for a custom thickness: one near the nut and one near where the body joins. Just specify which frets (and on which side of the fret) you are measuring.
The .9 inch measurement is the thinnest part, and it's taken on the nut side of the first fret. The thinnest you can specify is .8 inch. We need some room behind the truss rods for structural integrity.
Note, the thinner you get the neck carved, the less massive it will be. It will affect how much the neck moves in response to changes in humidity. You will notice the neck reacting to a smaller change than if the neck was thicker. This doesn't mean the neck of a thinly carved bass wiggles all the time, but it's something to consider if you keep your action extremely low and you live in an area with many swings in humidity.