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Removing it from the transom after taking the bolts out could be difficult if the installer had used a strong silicone, this was the case when I did mine.
Trying to pry it straight off could do damage to the transom, I would try twisting it off instead which is what I did and no damage.
As for the holes, I just put the bolts back in with a bit of silicone just in case I wanted to use it again.