The Residential Construction Performance Guidelines are not a mandatory standard, unless agreed to before the project starts. They are generally biased toward the builder (the tolerances are at the outer range of acceptability), since home builders wrote the standard in an attempt to resolve the exact type of issues you're dealing with. I have used some of the RCPG 'standards' in Expert Testimony over the years, basically because in most cases there isn't anything else! The building code (IBC) only addresses tolerance issues in a general way via workmanship provisions but does not spell out dimensional tolerances - unless it has some sort of adverse affect on the load carrying capability of the structure. So the building inspector will not have authority to force changes unless he referred the matter to a P.E. such as myself to basically declare the construction is - or is not - acceptable.
Your best bet is to look to the I-joist and subfloor (and/or flooring - particularly tile) manufacturer's requirements and see what their flatness requirements are. This is ultimately a fuzzy gray workmanship issue and it is up to you and the builder to resolve it, or hire an Expert and let the Court do it for you if you have a few years to waste. Ahh, the joys of building a new home
Did I tell you I hate I-joists?