The author never addresses the issue of trusting standard parameters. I agree with them on the rest, but standard parameters need evidence that they were not specially selected for reasons unknown to everyone else.
You're never going to get a satisfactory answer. The world's foremost proponent of not trusting standardized parameters wrote and repeatedly submitted a paper demonstrating a model attack that targeted curves built from mathematical constants; when you've "backdoored pi", there's really no place to go from there. That author's subtext, as I understood it, was that curves should be selected by functional optimization;…
If I remember correctly, part of the reason for the cofactor in 25519 is because Montgomery curves have to have a cofactor and only those curves have the nice x-only Montgomery Ladder, which basically rules out invalid curve attacks (so long as the curve is twist-secure — not all the NIST curves are IIRC). Do the complete addition formulas for short Weierstrass curves also fix this? Invalid curve attacks are a major danger for NIST curves.
I know you can use compressed point representation to get the same benefit, but that seems very rare in NIST curve implementations (because old now-expired patents). The landscape of NIST prime-order curve implementations is not great. If all those libraries were going to actually switch to complete addition formulas and compressed public keys then I might feel better about them enjoying a renaissance.