If for whatever reason they don't plan to replace the seat stay, I would plan to Dremel out some clearance and then epoxy the fibers. But really, I shouldn't have to.
If you plan to run a 200mm shock, I would absolutely contact them about it before it ships. Hopefully I'm just one of the first off the assembly line, maybe they've already caught the issue.
I'm thinking they'll simply add a channel to the arch in the future. Still have no idea how they missed this, it seems a pretty obvious omission. Maybe they did all their testing with a 190 shock.
That said, the rest of the frame fit and finish is top notch. It feels solid. And I really love the clever mounting hardware that allows for both trunnion and standard shocks. So far It's a great frame with one glaring defect. I hope they fix it going forward.
But yeah, it does make you wonder about what kind of testing the frames went through, if any. My thinking is they put it on a stress test machine, but who knows how it mounts to the frame.