Any advice?
Yep; contact SJS Cycles/Thorn as soon as possible, including this photo with your correspondence and save all packaging.
In my experience, they really do want customers to be happy and will be responsive to your inquiry.
I suggest keeping the packaging in case the scratch was caused by the carrier. If so, it may be needed if you need to make a claim with the carrier.
However, if the scratch was under the padding and not the fault of the carrier, then SJS Cycles can best advise what to do next.
As for the weld at the lower gusset...it is a little hard to see from your photo, but if it helps, the lower part of this gusset on my own Nomad is left open and appears much like yours with welds running along the sides.
I'm sure sorry you had this problem.
In any case, welcome to the Thorn Cycling Forum.
Best,
Dan.