You are aligning the cantilever/stylus. If the cantilever is not perfectly aligned to the body, if it were mine, I'd have it repaired or install a new cartridge. That is an indication of a defective cartridge.
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The alignment should always be based on the stylus/cantilever. Using the body is just an easier way for me. Just because the cantilever and the body are not in alignment does not mean something is wrong. I have seen new carts that are not perfect. My suggestion is to set it up and listen to it. If it sounds right who cares if it doesn't look perfect.