Fixing summary. Editable nodes are called "aliens". The "phantom" is the green hatched-out overlay that appears when mousing over an alien. It's an absolutely positioned <div> that exists outside of the main editor DOM. Because of the mouseover effect, you can't actually inspect the aliens themselves easily, but when you do, you'll find that the actual uneditable content is in <div class="ve-ce-alienBlock"> or <span class="ve-ce-alienInline"> as appropriate.

The issue here is that some things (nowikis in Raymond's example, and I've seen some references do it in the wild) are alienated as alienBlock nodes by ve.dm.Converter when they should really be alienInline nodes.

https://gerrit.wikimedia.org/r/39846

Merged; code will be deployed as part of the 2013-01-16 release cycle.