I'm a huge Kona Jake fan, and I don't have any experience with the BD cross bikes. I can tell you that a lot of people on the cyclocross forum are pretty happy with them. The biggest problem with the BD bikes is that you can't test ride them, so unless you really have your bike size dialed in, you've got a pretty good chance of getting the wrong size. There used to be a lot of stories about initial quality, particularly wheels that needed tensioning, but that seems to be happening less often recently (just based on my perception of feedback on this forum). You can't beat the price of the BD stuff.

You can't judge a bike just by the component spec. Frame quality is a very big deal, though nearly impossible to judge from specs. The Kona bikes are fantastic for racing. I don't know how important the intangibles that set them apart are for commuting. For instance, I've got a Kona Jake and a Surly Cross Check. For racing, the Kona is hands down better. For commuting, I really don't notice a difference.