When I talk about driving innovation with self-organizing teams, I emphasize that such self-organization includes expecting the participants to organize their own teams, give themselves their own goals, and determine for themselves how to measure their success.
In contrast, the definition of skunkworks points out that members of such teams are “usually specially selected.” Good thing he added the word usually – because specially selecting such teams throws a wrench in the entire works, limiting the value of self-organization and thus the ability for the organization as a whole to become more agile.