I purchased a M1898 that was missing the stacking swivel so I bought a swivel & screw.  I was struck by the difference between it (on the right in the photos) and the stacking swivel on another M1898 (on the left).  The replacement came in excellent condition; the one on the left has been squashed a bit.  Still, the difference in the depth of the two is substantial, about .06".  Is the difference solely due to the one being squashed or were there variations in the swivels?

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I believe it is just the squash. The one has not only been pinched to a smaller radius, but the arm with the lug is actually deformed as well, on both sides, though one is more pronounced than the other. Aside from normal manufacturing tolerances, I know of no intended change in the swivel.