If you get no other inputs, and if this were my own job, I'd be doing what you're thinking.
Looking at your colored drawing, I would think that the blue "filler" would be pretty necessary for good distribution of the load between the base of the tower and the top of the gunwhale. But how would I contour the profile of the upper surface. I have a lot of machinists at my disposal. Without them, I do it by hand. I'd pick a soft aluminum plate, a belt sander machine, and a lot of emery cloth (or the like) with an adhesive back. I'd rough shape the upper surface profile on the belt sander. I'd finish by tacking the adhesive backed emery cloth in the channel of the base of the tower, and sand it off by hand to match the channel of the base of the tower.
I'd also do this. Between the base of the filler and top of the gunwhale, I'd put a thin sheet of (tough) elastomeric material. Silicone rubber? SBR? I'd have to think about that after some research.
More importantly, between the undersurface of the gunwhale and your washers and nuts, I'd build an elongated plate to elongate the distribution of stress introduced by the washers, to over a much greater contact area across the underside of the gunwhale.
I'm pondering what I'd do at the interface between the filler's upper 'profiled' surface and the tower base's channel. I'd like to lock them solid somehow. Fasteners?
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