Earlier quoted context omitted.
Overlaying on existing infrastructure is a faster way to get up and running, but ultimately a darknet that depends on another network is vulnerable to that network's centralized 'off' button.
See, that's what I didn't get about the article: DARPA intended the Internet to be built against single points of failure. Where is the Internet's 'off button'? Sure, there are exchanges and backbones that are more important than others (e.g. LINX in London), but it takes sustained and continuous efforts by a government to even come close to filtering/censoring the Internet effectively.
Yes, and they (government) are the sort of people who sometimes want to censor speech & the internet. Some countries have filtered the internet before, this is not an abstract problem.