Remove the bolts, then using a small artist brush apply thin epoxy onto the exposed edges of the bolt hole in the plywood and let it cure. That will help prevent moisture from wicking into the end grain of the plywood. Next reinstall the bolts using marine bedding compound inside of the plywood holes. The bedding compound will also keep moisture out of the layers of plywood as it takes up the space between the bolt and the hole in the wood. As you push the bolt in and tighten it down the bedding compound will also squeeze out from the hole and seal the area between the frame and the
fiberglass. The bedding compound is a good choice as it last for a great many years while allowing the bolts to be removed if needed.
This method will serve you a lot better over the lifetime of the trailer than relying only on an application of caulk. There is a lot to be learned from how water is kept from entering a boat