Not sure exactly what you are working with, but I would use heavy fiberglass cloth and resin to bond new transom to hull, and only use putty to fill voids.
I would consider using epoxy resin and cloth, if I have any doubt about strength of repair.
I would think that stuff is similar to the PB mixture we all make with resin ,cabosil, and chopped fibers ..
I cant think of a reason it wouldn't work but making your own would be more cost effective seeing as your gunna need it for fillets also ..
