Sure hope you have a mechanical inspection before any of that gets covered. Believe your on the IRC there. The flex, per mfg. installation instructions is to be supported every 4'. Its also to be 1 1/2" wide on the supports. Now wwhen its in the rafter span roofing nails WILL penetrate the vapor barrier. Its already crushing the flex where the drive cleats are being used as supports. Can't read the R Value on it in the pic but my IRC says that in the rafter span it needs to be a minimum of R-8. As far as runing across the floor it does look like a window seat was planned. If not have em move it. Get it inspected, sit down with the builder, but by all means call your attorney for advise before hand.