While I don't necessarily subscribe to the "moon = spaceship" theory, I do find this last comment about the black moon being inserted in the white moon compelling. Mainly because it would be a strong Freudian analogy.
Just look at it this way:
The white moon is huge, fertile and stationary. Female, like an ovum.
The black moon is smaller, carrying the seed of life and mobile. Male, like a sperm.
The black moon merging with the white moon could very likely be the symbolic cosmic "conception" of the new "higher" form of life that NERV would have been after.
Further clues:
- The pockmarked surface of the Black Moon would indicate that someone somehow prevented the Black Moon from rising during Third Impact. It might have been WILLE.
- Fuyutsuki calling the Black Moon's crash a giant mess and saying that it was exactly as SEELE had intended, would indicate that the (further) rise of the Black Moon was not intended by SEELE.
- Fuyutsuki's regret, and Gendo's subsequent comment marking the event as an acceptable loss (since he had gotten several short-term gains out of it) illustrates that NERV does want the further rise of the Black Moon.
- Symbolically, NERV symbolizes the Freudian male or father figure. NERV were in control of the Black Moon, giving it a male connotation. (Also, note that in Rebuild 2.0, Gendo and Fuyutsuki were not allowed to actually reach the moon in their spaceship.)
Speculation:
- Perhaps whatever that Key of Nebuchadnezzar unlocks is on (or inside) the (White) Moon. SEELE appears to have taken strict precautions to keep Gendo away from there from as early as Rebuild 2.0. And this as good a place as any to repeat that I believe that Gendo was a prisoner at Neo-NERV base, with Kaworu his jailer.