After the things I have seen from boat builders I think most would do a better job. Almost a plus in my mind if it has been replaced by a quality shop.

when replacing a transom and stringers, if the top part of the transom is in good shape and the bottom rotten, it is better to just replace the bottom or is it better replace the whole thing. i can see pro's and con's for each;

replace bottom - top of stringer keeps the boat in it's original "shape", less to replace, less expensive?

replace the whole transom - all wood is solid & new (assuming a new product is better than one at manufacture), seems like a lot more work.

sort of thinking out loud here...

you need to replace the whole transom in order to obtain best structural integrity IMO, in any case not much more work to do it all. the bottom and the stringers are where the work is