I think you are mistaking discoloration for rust. The keel bolts and nuts are stainless steel. Once you have dewatered that area completely, give everything a good scrub with warm, soapy water with little bleach and look at them after everything is dry.
I think you'll find that they don't look the same.
I routed the 3/4" discharge hole along the inside of the hull out of the bilge and then diagonally over to starboard to enter the area between the inner liner and icebox area. I cut a hole there in the vertical part of the inner liner in that open storage area below the companionway. This was sized for installing one of those removable inspection/access plates (like the one in the aft area of the cockpit (transom).
This allowed me to grab and pull the hose further aft. I went into the lazarette and bored a hole next to the one there for the exit of the manual bilge pump hose and then routed up to a thru-hull. There were no existing holes in this area of the hull.
I'll see if I can snap a few pictures this weekend.