There has been no public acknowledgement or reasoning provided for the resequencing. The general consensus is that it follow the original source material format better.
In short, this newly assembled cut of Sin City more closely follows the path of Miller's original series in two ways: not only does it re-insert a few minor scenes back into the film, but it also allows the viewer to watch each "chapter" individually (or in the sequence of your choice)---so it's more like reading the actual books than ever. This, of course, improves the overall experience, especially since Rodriguez and Miller were aiming for pure accuracy in the first place. Sin City has evolved into something else entirely by making the chapters more "interactive", moving it one notch closer to the most faithful cinematic translation of a comic book ever. With any luck, it'll be considered the blueprint for the genre---at least in the technical sense---for years to come. The original cut was close to perfect (and this one's even closer), but just what's been added to the film itself?
Though Buena Vista's promise of "over 20 minutes of additional footage" falls short (more on that later), fans are treated to a handful of scenes that were previously seen only in the original books.
REASON FOR MULTIPLE VERSIONS:
Technology more than anything else. There’s certainly no great narrative reason — Dimension didn’t force Rodriguez and Miller to lose one of their short stories for the sake of a more commercial runtime or anything like that — nor are there any major censorship concerns. In fact, even though the “Sin City” Special Edition’s “Recut, Extended, and Unrated” cut boasts that it is, yes, unrated, it doesn’t contain any significant additions of violence or sexuality. I’m quite sure it’s unrated only because Dimension didn’t submit it for a rating; if they had, it surely would have received exactly the same rating as the Theatrical Cut. Mostly this is just Rodriguez, a guy who loves big DVDs with comprehensive special features, giving the hardcore fans of the film an extra version that breaks up the film’s four stories and presents them like individual episodes in an anthology mini-series.
The Special Edition DVD has multiple director commentary tracks, but I didn't hear anything explaining the recut.