Whether or not the floor was PERFECT - the fact that the basement floor is 5 freaking inches higher than it was supposed to be would be a dealbreaker for me. That's not even close to what you asked for. Ceiling height is a a premium in most basements - 5" is a LOT!
Based on the way you are describing this guy it doesn't sound like he is willingly going to come in and bust it up and do it over - may be time to lawyer up.
I'm not sure how much help the inspector is going to be able to give you on this one, other than possibly re-assurance that the floor is "non-conventional" at best. As far as code, I can't imagine any state has a max. thickness or it's against code to pour 2 layers, even it it's a bad idea. Also unlikely you'll find any standard protocal for flatness of residential floors.
Any chance your blueprints have a cross section showing the proposed height between the finished basement floor and the bottom of floor joists? Or at least the finished floor height in relation to the existing basement floor?