There is no standard for the axle to bottom headset height. There are too many variables- tires, fenders, brakes, standover height, etc.
For the rest, as always, it depends!
Depends on what kind of jig you're building/depends on what kinds of bikes you're wanting to build.
My jig has fixed reference points for the front and rear axles and adjustable head tube/bb heights. This way it's super easy to set up and can build all sorts of frames.
I've used several styles of jigs and I think this rail type is the best!