Drilling a hole in carbon goes a lot smoother with an abrasive cone shaped dremel bit. The one i use is just over 3/16 at the fattest part of the cone. a drill bit breaks away fibers and leaves a mess on the inside wall just as drilling a hole in plywood without a sacrificial backing board would do.
i know aluminum and carbon + salt water almost makes a bomb and thinking you can do a barrier with some glass is overly hopeful in many cases. It's news to me that good stainless would react at all with carbon. It's stainless and not supposed to react with most other solids.
Also do rivet sleeves like they use on Hobie cats help?