Thanks for sharing this experience. I'm sure you're not alone.
This strikes me as a fall-out of the effort to scale-up certification capacity--which means more of it is done by people who are following the letter, and not necessarily thinking it all through logically. Hopefully GBCI's recent decision to stop using certification bodies and manage all the certifications internally (with outside reviewers, like USGBC used to do), will help bring some common sense back into the process.