There is no automatic way to do that. You'll need to carefully photograph the product so that the Logo is very close to the same size in each shot, but not in the same position in the frame. This includes ensuring that the logo's angle to the film plane is the same in every shot. Then, set the Anchor Point for each image in the same spot on the logo. You might pick the top left corner of the design.
Then, every layer's position would be set to the same value, and each layer would be rotated and scaled so that the logos match. Using a Blend Mode like Difference would make this alignment easier. The Blend Mode would then be reset, and you would make the cuts. Parenting all layers to a Null would allow you to move in and scale the shot to simulate a camera move.
Nothing magic in the technique, just a lot of careful planning and manual work.
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