To remove and replace the transom from the outside, you'll probably be wrapping glass onto the lower hull which may change the profile of the hull bottom.
Other then some cracking, whats the motivation to do it from the outside?
If the transom is shot, the deck and stringers need to be well inspected so there is likely a good but of work on the interior side anyway.
Fill and fair or other cosmetic repairs on the outside sounds like a small bit of 'extra' work if you have interior work to do anyway. Rather then do interior work and then cut the transom out from the exterior too. That'll be lots of structural work then lots of fill and fair to blend and transition the new glass out onto the hull sides and bottom after you wrap the glass over the edges of the transom.
Lots of great info in the resto forum. Dig in, it'll be helpful once you get to both the tear down and put back stages.
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