I suspect that you will find two schools of thought. The guys who recommend encapsulating the wood in epoxy and those who recommend sealer/primer followed by a good enamel paint job. For a tin boat transom I'm in the non-encapsulated group because the wood is never going to be submerged for significant periods of time. The drain plug is below the wood as is any bilge pump arrangement if your leaving her in the water. This arrangement gives the wood plenty of opportunity to dry out after it gets wet. In more detail what Ive done is mount the wood to the aluminum with a silicone sealer (I stayed away from the 5200 in case the wood needed to be replaced in another 25 to 40 years). Do make sure the sealer is rated for aluminum as not all are and those that are not will attack the aluminum. This sealer layer was used because my old wolverine had lots of screws attaching the wood to the transom and I believe as the bolts are tightened the sealer is squeezed into all the fastener holes minimizing any water penetration at the fastener holes. It will also help prevent water from getting between the wood and transom when you drill the motor mounting holes. As far as gluing two sheets of marine ply together, like Dave I would recommend epoxy although I suspect any of the Titebond or Resourcinol waterproof glues would work well.
Have fun,
Scott