Well I don't have Frank in front of me, but the easy way to dismiss the USSBS is to point out that its conclusions were very motivated by local political circumstances (they were trying to make the argument that conventional strategic bombing had ended the war, and to use this as an argument in favor of a large and independent Air Force), and that they go beyond the evidence that they had available. (Even a "revisionist" like Barton Bernstein agrees with this.) The USSBS is one take on the end of the war, and not necessarily the most impartial or omniscient, and they were limited to their not-always-compliant relationships with the Japanese who were by then under Occupation.

The modern historian has access to far more sources than they did, in other words, and nobody takes the USSBS as the last word on any of this. That doesn't mean that their conclusions aren't ones one can come to — but you don't take the USSBS report as evidence of those conclusions by itself. I find the USSBS report useful as an illustration of the idea that these things were controversial almost immediately, but beyond that it is something that needs to be treated as a tricky primary source of its own.