Lots to unpack here and it's late but I got pretty familiar with this roofing in Baytown after Harvey. Every roof required certs.
If you are in a windstorm area, this is non negotiable. Check for yourself to verify, don't rely on some yahoo at the insurance company to tell you. They don't know and they won't back it up if they are wrong. Trust but verify.
The hand nail requirement isn't necessarily required and you will pay for that. It takes longer, it doesn't result in a better job, and labor isn't cheap. This will depend on your engineer. My engineers then wanted hand nails. My engineers now in this area will pass my roofs with hand nailers because we calibrate frequently and he will check for overdriven nails. I install 6 nails per shingle, and we follow his requirement for hip and ridge nailing and mid roof inspection, underlayments are installed to spec, drip edge is overlapped properly, etc etc etc. . If any of this gets screwed up, you don't get a cert, no TWIA joy.
Make sure the roofer knows this process. This isn't a "throw on a roof and move on" kind of deal and I saw a LOT of roofs that supposedly had windstorm and they actually didn't because it wasn't applied for, or inspected, or passed, or any number of things. That's the suck when it comes time to make a claim.