I don't know what it's like where you live, but here building inspectors are gods. They can make any stupid decision as long as it's remotely backed up by code. My husband's a structural engineer and deals with this stuff all the time. Not long ago, he was dealing with a situation where the building inspector had misinterpreted some code and given my husband's client nonsensical stipulations. The easiest thing to do was just go with it.
I suspect you'll have a really hard time getting an engineer on this. My husband's office is one of the few in the area that does small residential stuff like you're doing. They basically do it as a public service because it's time consuming (especially alternative stuff where the code isn't written for it) and they don't make any money on it.
I'm guessing that now that you're at the final sign off, someone at the office is looking at your build as a whole, rather than each individual stage, and thinking, "Hang on. This is a little out there. Are we sure we want to be liable for this?"
I think Bruce's idea is good. Also, they might just want a professional on record (someone, anyone!) that they can shift liability to, so you might be able to get creative with the type of professional and use someone unconventional.
My husband suggests forging something 🤣 If they just want to check a box on a form, they'll never look up Enemabag Jones's credentials. He also suggests just moving in and seeing what happens. They won't issue an occupancy permit, but maybe they'll never enforce anything. If anything happens, they just want to be able to say, "Well you don't even have an occupancy permit, so it's not our problem."
Keep in mind my husband and I both come from families with traditions of thumbing their noses at building inspectors, and we've carried on the tradition by not getting anything on our property permitted. We may give seriously bad advice 😁