"Hi Clayton, so you mean you want to do the entire process without any user interaction at all, not even selecting an outline of the hole to remove?"

^ Yep! I was hoping I could get away with it. So far I've gotten internal holes to work the way I want them to, but these split holes made up of two faces have got me stumped. I'll look into some research papers about feature detection to see if I can decipher and apply their secrets.

After reading up on the topic here on the forum, it seems like their isn't a way to filter edge selection based in surface continuity to be able to target all "hard" edges. Would you please confirm this as the case?

Thank you for all your replies! I'm no where close to a genius, but I'll do some research on white papers as you have suggested.