Jailbreaking is not a violation of the DMCA per se. However, if you read the article, it seems that Apple checks whether applications that have been copied illegally would run on the device, and in that case iBookStore doesn't run. So they are explicitly checking for a device that _is_ in violation of the DMCA.
Exactly. You might be legally allowed to jailbreak your device (as the LOC DMCA ruling seems to imply), but if you also want to run Apple's apps or App store apps, you may have to lock it back up so that it can't run apps whose modification would be a different violation of the DMCA (not under LOC protection).