I received my Kirk 5D3 L bracket and was quite disappointed that I have to remove the left strap so that the camera strap hook can sit nicely in the L-bracket. There is simply no allowance for the strap thickness in the bracket recess for the left strap hook.
You should use that screw on strap connector for the neck strap, it also adds extra connection/reinforcement point. Kirk's item description on web site is very clear on that.
Not sure how you managed to get those marks on the body, I can assure you it would be much, much worse with RRS as their flange in not rounded. Properly aligning plate before tightening it down would have help avoiding that, I guess.