I think the authors of the presentation† would agree with Schneier about the math, and I know Tom Ritter's working on a bit of a follow-up. But I don't think they'd agree on Schneier's message here, which is that people who use RSA have nothing to worry about. The Joux small-char DLP stuff isn't going to directly impact RSA, but RSA in its most commonly used key size (1024 bits) is not secure, and the next common size up (2048 bits) is ~5x slower. It's past time people started moving away from RSA.
† My name is first listed among them but I did literally no work on it; I'm as confused as you are, but flattered.