Originally Posted by Andrew R Stewart

I applaud the thought of having a through hole for two reasons. You have two options for where the rack braces connect to the stay (in or outside) and the hole is a through hole (allowing threading repair in the future). I wouldn't be too worried about strength loss in the stay as long as the boss is at least 1/2 the stay's diameter and consider having both ends flanged (a washer would work well).