Hey JC, I've got the new dierks through transom setup and am currently just running a 16 lbs mushroom anchor. It likes to bang on the transom a good bit even with zero play in the knot. I'd think the extra distance of the pulley between the rope and anchor would give you a ton of anchor swing. You may be fine with a pyramid style anchor though. Anyway I just screwed on a 1/4" piece of Sintra which is like a really hard pvc foam and covered it in copper for a classy bang plate. As far as a place to mount the static end of anchor rope you could get creative and find a nice flush mount tie down to set into the transom or just drill a hole and bolt in an eye bolt.
The floor mount for the foot pedals is wedged in really good between the frames and the bottom so thats a pretty sturdy place to be. I was worried about the stress on the bolts like you but now its a non concern.
Dierks will bend you a mounting bracket for the foot release that fits between the frames if you give them the distance.
I bolted the release to a homemade wood bracket then bolted it to the frames. Just #10 bolts (3/16) I had left over from the gunnels
yeah its mounted to a bracket that is squeezed between the frames and bolted. Nothing moves but the anchor rope