The great thing about wood/epoxy construction is that it's easy to fix things, especially cosmetic damage. I wouldn't worry about doing anything special to protect the transom--assuming you've glassed it. As Tod said, once you've got the transom height right for the motor, go ahead and drill the holes and bolt it on. You might want to put some 4200 on each end of the bolt to keep water from soaking into the wood along the bolts. That's really the only precaution you have to take.
If someday you change motors, as I did with my Bluebill, you can fill the old bolt holes with thickened epoxy, and even fair the depression from the clamp rings with epoxy and microballoons. Put a fresh coat of paint over it and it will look like a brand new transom.
Rick