The shaft won't gain any weight, or spine, by cutting it. The difference is in the dynamic spine, which is how it acts on the bow. Theoretically, you are correct, that by cutting the shaft shorter you are stiffening the dynamic spine, but it won't show up on the spine tester. It's the same stick, after all.
What's your point weight? Where does the arrow impact the target? Where is your nock point? If it's too low, the arrow could be "bumping" the shelf on its way by, screwing up all your careful testing.