i think i follow what ur saying doc. to fill that gap, if i chose that route, i would find my nearest spray foam insulation contractor and have him fill that void wth closed cell (rigid) foam. would prob be cheap if you could pull ur boat to a jobsite where he is already spraying. then reclass the cap and no worries.

keeping in mind that this will not fix any wet or rotten spots that already exist in ur transom. nor will it raise it any. if you do wanna get it rite, like you said, nows the time.