That green stuff is Plexus adhesive, and it is squirted down in lines like it came out of a giant calk gun. You just didn't happen to run into any with the hole saw. There are other places where water can get between the hull and the liner, like where the drive shaft goes through the boat, and where the through hulls for water intake are, etc. I don't think it is a huge deal that there is a little water in there. Lots of boats have no liner at all, ours are kinda deluxe like that. I think it is mostly cosmetic, and to make the bilge stay drier and cleaner.
So, HiFlyin, does your throttle assembly look like the ones in my pics? I'm 99% sure that Cal's is different because of Accuski, it just means he has to remove a few parts.