The FBF and DP tools, at least, are supposed to be identical and interchangeable, and every time I measure mine I get the same answer to a fraction of a millimeter. That's why they make those tools, and why basically all tuners use them.
You have to use them consistently - what I do is measure from the top flat surface of the left rear nut (rotate the wheel until a flat surface is on top, level with the ground) to the top edge of the gauge and then add 20 mm to get the ride height measured to the center of the axle. If different tools give measurements different by more than a couple mm, something's wrong with one of the tools or with the way the measurement is being done.
On my 996 I'm currently running 257 mm (top of tool to center of axle), which is a bit higher than I'd like but I can't go lower without swapping ride height adjuster bars (I'm using the lower straight-rate linkage hole on the two-hole linkage that came with my Marchesini swingarm). My 748 street bike is at 250 mm, with stock everything. If you poll folks like Nash, Meyers, Jenkins, etc., you'll find typical recommended numbers in the 250-260 mm range. In my experience, going higher tends to kill rear-tire traction and front-end feel unless you also raise the front end a bunch, which raises the CG and makes the bike feel tippy and hard to pick up. But it's partly a matter of personal preference.
There are so many variables it's amazing! It's kind of like dynos, they atre good for a before and after, but a direct comparison is not exactly science.
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