Very common with I/O's. See how they expoxy and glass the large cutout? They don't do this with bolt holes. They rely on the caulk. If the caulk breaks down and water weeps in, it will soak into the balsa coring first.
It's tough to call this preventative maintenance. Hauling the engine, then removing the drive in order to remove and rebed the transom assembly is not really 'preventative maintenance'.
I can attest that things that can impact the caulk around the transom assembly are vertical and horizontal loading of the transom assembly. This can be caused by grounding the outdrive in shallow water, hitting submerged objects, and hydofoils.
This is fixable. You'll need to remove the fiberglass skin on the inside, then hog out the rotted wood. REplace with marine plywood, re-epoxy and fiberglass, then seal with an expoxy paint like a vinylester resin.