I've read the usenix paper, and I'm reasonably sure I'm right. Care to elaborate on what I'm mistaken about? I (and a few other people I've talked to about schemes isomorphic to this about) may learn something new :-D
Basically, the assumption that bcrypt is just a function that returns a hash oversimplifies the detail of how salt is stored in practice.
I agree: this is not a big deal in practice. bcrypt with a cost factor of 10 is so much slower than SHA1 that this is just not going to be an issue.