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The two holes are there to help you remove the old seal. Using a small punch, the old seal can be tapped out using these holes. I wouldn’t be too concerned about the thickness of the new seal. As long as it’s installed square and keeps the water out, it will be fine. Bottoming it out in the carrier might even help the seals lip to ride on a fresh part of the shaft. These gearcases have been apart before and the seal carrier wasn’t aligned correctly with the corresponding dowel in the case before everything was tightened down, thus leaving the imprint.