The only difference on a federal site is that the AHJ typically has a vested interest in that site. Depending on the site, they may not even be an expert, they may just be the responsible manager. It's easy for the city AHJ to fail you because he doesn't have to face any of the reprocussions. But when the inspector has to pay the repair bill for any violations they find, and take the heat for any delays and other problems... they apply operational risk managemant and tend to 90(C) a bit more liberally than one who completely ignore the whole "economics" and "operational impact" portions of the equation.
To the FAA, the difference in cost between 1x 30A and 2x 20A is negligible- there's nobody out there who's going to risk his neck and his facility for the sake of saving $200. At least among those AHJs who understand the risks involved. They may simply not be aware- I know it's hard to believe, but engineers sometimes make unintentional stupid mistakes, too
I'd raise it as an issue of concern and let the engineer and AHJ make the decision. If they're OK with the risk and say go and give it to you in writing, the design is legal and you're OK.
FYI, I work for the DoD and hold AHJ responsibility at a number of federal sites.