Ah, but that's why I posted that particular project: The guy figured out most (maybe all) of those problems. Skim through the comments and you'll see that he at least thought about them. In particular, he's using strong lights rather than a flash, which avoids the glare in the same way that those enormous photography lamps avoid red eye. Also, the entire point of building the rig is to fix the perspective problems, so much so that I'd be willing to bet that one of the steps is something like "measure really, really, really carefully."
The sample book also looks pretty nice (as do almost all of Google's scans, by the way).
Again, I'm not suggesting that everybody run out and start a construction project, but I figure there might be someone interested in tinkering to see what kind of results we can get.
The biggest potential pitfall I see with a comic book, though, is that you can't rely on the gutter being empty; any content near the spine is going to be at the intersection of the plates, and obviously difficult to image.