What I meant by "distance is distance is distance" is that deflection is a measurement of length (distance) only. It can be in millimeters, inches, feet, fathoms, or whatever. You can measure that distance with a tape, a dial indicator, sound waves, lasers, whatever you want. Unless you are doing it wrong, you will get the same measurement no matter what tool you use.
Deflection tests also have to have a force and geometry either specified or implied. Take arrow spine for example. It is assumed that a 2-lb weight (the force) is hung from the center of a horizontal 28" simply suported span (the geometry). Deflection is the distance from the midpoint of the shaft at rest to the same under load. The end product - the deflection - is only a distance.
The only thing that makes sense for a bow limb is to rigidly supprt the riser end the same way it is supported in the bow and apply force in the same direction that the cam would. How you accomplish that makes no difference at all to what deflection measurement you make.
Is there some standard you are trying to figure out, like an ASTM or IBO standard, or are you just trying to fabricate an apparatus for measuring limb deflection to satisfy a curiosity?
I would take the strings off the bow, clamp the riser to a board, and pull the limb at the axle with a spring scale. Put marks on the board for various weights, and voila, you have a handy-dandy force-deflection curve for your limb.
Scott