Wood is used in boat transoms for several reasons.
Here is a pretty good explanation by one boat repair facility
http://www.starboardmarineinc.com/Home/materials
I'd use wood (the right wood) if I were fixing your boat.
I know for a fact that Lund and Crestliner use "Marine - Treated wood". (no copper, no arsenic).
As for what other brands,--I have no idea what some of the other brands use for wood in their transoms.