Transom Repair

Anyone have any experience injecting epoxy or foam into a transom? I have an old glass boat that has several spots where transducers and a swim ladder had been installed but not sealed correctly. This has resulted in a few localized spots where the wood has started to rot. My plan was initially to cut large holes and fill the void with epoxy but I'm seeing where a lot of people are using epoxy in caulk tubes or something like injectadeck to inject into 1/4" holes in bad areas areas..
Just looking for guidance, epoxy seems smarter, but at the same time the foam would deal with the water better.. Thanks for any advice.