I read your article. Interesting. Just by looking at this picture:
There is a small black washer (rubber) underneath the washer that sits under the head of the set screw. It looks to me that the bolt was over tightened. Perhaps, and I repeat, perhaps when Dagger assembles their boats they would use pneumatic or electric screw drivers etc to speed up their assembly line. (like most assembly lines in other industries) It is possible that whoever tightened this screw way over tightened it. With a pneumatic driver it is pretty easy to do that and given a fast rotation of the screw itself and the washer, it would have heated up during that process and hence and black residue still evident and also the recess which it has created from heat (maybe just a tiny bit) and of course the mechanical damage created from them over tightening it.
Of course this is only speculation on my behalf.
(As a side note I should add that Wave Sport and Dagger are made by the same company (Confluence) and I had 2 Big EZ's crack in that exact position. My situation was different and it cracked due to another reason. The reason being that once you sit in the boat, the distance between the bottom of the seat and the mounting plate was LESS than the distance from the bottom (inside) of the hull to the mounting position. This caused the seat to effectively HANG off of the actual hull of the kayak and therefore induce a major stress concentration on that area. First boat cracked after about 8 months and the second under 3 months. Both times the boats were replaced, free of charge, no hassles.)
I can only guess that it was an assembly error and they should replace it. Or repair it but not as good a option. Let me know what happens. I'm surprised they have ignored you this far. Maybe mail them this link and yours too as bad press for any manufacturer will make them think twice before shaking you off.
Just my thoughts from working in manufacturing environments and seeing similar things happen.

Good luck