From my experience with this issue I will give what insight I have. From dissecting a few of these I will tell you the seams are there and were not glassed for a reason and covered with trim. The Tsunami is a 3 part hull and there is a certain amount of "float" between the cap and deck. It is nessarsary as fiberglass boats must flex and joining these seams causes other complications. How do I know? Mine were glassed when the deck was raised and over a short amount of time the stress was transferred to other areas requiring much more additional glass work to rectify.
Potter putty was not some bad idea to take shortcuts but a material used to close gaps and provide support between the three hull components ( hull, deck/liner, and cap) with one of the functions being to allow tolerance for movement due to hull flex.
To me the issue seems to be with the core material which you are fixing. My recommendation is to not connect the deck and cap in anyway unless you want to do more extensive glass work that will render a less than factory look. Matching gel coat will be the least of your issues.
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