jk I’m sure it’s fine… probably
I still think it's probably fine, but I feel better about insisting on SHA-2+mitigations or blake3 instead now, even if the main problem with SHA-3 is its being deliberately designed to encourage specialized hardware accelleration (cf AES and things like Intel's aes-ni).
Do you think he’d disclose it if he did?
Making late (in this case, after the competition was already over) changes to a crytographic primitive - without extensive documentation both of why that's necessary (not just helpful) and why it's not possible (not just you promise it doesn't) for that to weaken security or insert backdoors - is a act of either bad faith or sufficiently gross incompetence that it should be considered de facto bad faith.
Schneier claiming to believe that it's good faith implies that he either doesn't understand or (presumably more likely given his history?) doesn't care about keeping the standardization process secure against corruption by the NSA, which suggests either incompetence or bad faith on Schneier's part as well. (Or, in context, that someone was leaning on him after the earlier criticism.)
This is particularly inexcusable since reducing security parameters on the pretense that "56 bits ought to be enough for anybody" is a known NSA tactic dating back to fucking DES.
From your first link:
I misspoke when I wrote that NIST made “internal changes” to the algorithm. That was sloppy of me. The Keccak permutation remains unchanged. What NIST proposed was reducing the hash function’s capacity in the name of performance. One of Keccak’s nice features is that it’s highly tunable.
I do not believe that the NIST changes were suggested by the NSA. Nor do I believe that the changes make the algorithm easier to break by the NSA. I believe NIST made the changes in good faith, and the result is a better security/performance trade-off.