I didn't know there was different bonnets...?
Regarding nearlythere issues:
It sounds similar to the problem I had. My ute wouldn't exit theft mode even after a full key re-program & PATS reset. (With 2 factory keys)
But as soon as I plugged in a new (2nd hand)
BEM & ran the keys & PATS program again, it started first try.
Haven't had issue since.
It was a bit of a gamble...but it sounds like you've eliminated most other things?