Basically citations probably aren't going to be terribly important to most wikis, even if they do have the extension installed, so having the citation menu in the general insert menu will make more sense for them. For projects where citations are much more important (such as wikipedia, wikibooks, and wikiversity, in the wikimedia configuration), the config allows them to move it out.

Essentially just swap the default in the extension. Apparently this won't even affect wikimedia because they're all specified anyway in the wm config.