in days of old with small aluminum runabouts, fishing boats and utilities, there was a small wooden pad on the outside to prevent marring of the aluminum when you installed and removed the clamp-on motors. it also made the transom thick enough because there was only a 2x10 or similar as the transom wood.
i have seen that replicated in aluminum, however always looked best as a section of ash or white oak.
some early fiberglass utility boats had the same pad
larger fiberglass boats with proper transoms do not need it. the motor is bolted in place
the big patch panel because the transom is rotten is simply someone putting a last ditch band-aid on a rotten transom. especially if the motor is bolted on properly
rubber wont help here, for vibration either because to make the joint rigid enough for the bolts to do their job, you have to compress the rubber solid